Changing Tides of Atlantis
by Anjirika
Summary: -Spoilers for S4 & S5- "Colonel, we lost Dr. Weir on the replicator planet. Can you lock onto her locator beacon, beam her up?" How would the seasons have changed if the reply was 'Yes' PLZ R&R -Previously 'What Would Elizabeth do'-
1. Part I: We Have Her

A/N- This is the way Lifeline SHOULD have ended. Note, the first line may belong to TPTB but the rest is all mine.

We Have Her

"Colonel, we lost Doctor Weir on the Replicator planet. Can you lock on her locator beacon, beam her up?"

The desperation in his voice wasn't well hidden as Sam scanned the planet amidst the pounding of the Replicator ship. At first there was nothing and she shook her head when suddenly the console beeps.

"I have her signal." Sam answered happily. "Beaming her to the bridge now..."

All eyes went to the front window where there was a flash of light. When it died down there was Elizabeth Weir, looking no worse for where.

"Colonel Sheppard." Sam answered joyfully. "We have her."

In the jumper as he pulled into the 302 bay John felt a huge tension lift from his chest. "Copy that," he stated.

----sparky----

He had a single minded purpose, to get to the bridge as soon as possible. He practically ran the entire way there with Rodney and Ronan close behind. He had to make sure that she was okay, he had to make sure that she was alive and then suddenly as he rounded a corner John saw her walking towards them.

They both stopped for a moment. Relief spread across both their faces as they saw that each other was alive and well. Rodney and Ronan came up behind John while Samantha and Colonel Elis came up behind Elizabeth but before any one could say anything both John and Elizabeth crossed the distance between them. And just like when John was returned to her during the siege, she threw her arms around him. Only this time, he reciprocated with as much emotion.

Not caring about the eyes of the people around them, Elizabeth and John held onto each other as though the other was their one and only lifeline in the world. Elizabeth buried her head in the crook of John's neck and John in turn tangled his hand in her hair. He could feel her trembling slightly and decided that he needed to look into her face.

They broke the hug at the same time, and the result wasn't awkwardness, just understanding. Their eyes stared at each other and he nodded. "It's good to see you."

"Yeah," Elizabeth whispered nodding imperceptibly herself. "It is good to see you too." She sighed and shook her head. "I thought-"

"What you did," John interrupted. "Was incredibly stupid, and brave and-"

"-and it worked." Rodney interrupted coming forward. "We got the ZPM."

"That's good to hear." Elizabeth replied with a small smile before turning to face Colonel's Carter and Elis with a thankful look on her face. "Thank you, for getting me out of there."

"I almost didn't have a lock but-"

"But you got her." John interrupted, causing Elizabeth to turn back to him and he smiled his usual smile only Elizabeth could see that it was the same one that he reserved for her. It was the same smile that he had given her during her first incident with the nanites when John had thought that he had lost her. They held the gaze for a moment before John looked back to Sam. "Thank you."

They all had their Elizabeth back, and no one was gladder than John.


	2. Part I: New World

A/N- A coda to Lifeline (well my version of it) how things would have played out had Elizabeth been there. As before, some lines belong to TPTB other belong to me.

**What Would Elizabeth Do?**

New World

They made it back to Atlantis and plugged the ZPM in. The shield was back at full strength and imminent death had been postponed once again. The last order of business for the Atlantean crew was to pick a new planet. In the control room John, Rodney, Samantha and Bill were all looking at a wallscreen that projected a list of possible planets.

Rodney pointed to the screen. "Here's a good one. M35-117."

"Does Dr. Weir know about it?" Sam asked turning to the scientist. "In case the Replicators got anything from her?"

"Well," Rodney began mulling his answer over. "It's not on our primary, or our back-up lists. I purposely searched for planets we'd never considered before. If the Replicators got anything out of her, they uh- won't be able to find us because we've never considered this planet before."

"That's good for us." John stated with a grimace, his mind far from the discussion at hand and several levels down where Elizabeth was being examined by Dr. Keller.

"Yeah," Rodney agreed with a half-hearted smile. He along with everyone else knew how close they had come to losing their leader and what made matters worse, she was still half-replicator and would have to deal with that for the rest of her life. "Look-" Rodney began again pushing all distractions from his mind. "It has a stable atmosphere a uh- big ocean and besides the large particularly venomous snake-like creatures that inhabit the mainland, it looks to be a rather welcoming environment." Rodney looked to John for approval. "Do we have a go?"

John didn't say anything, he merely nodded anxious to get down to the infirmary.

"Alright," Rodney said as he activated his headset. "Radek, how're we doing?"

----sparky----

They were still in hyperspace when John went to visit Elizabeth. She was no longer in isolation and was now in the main area of the infirmary. She sat up with her laptop in her hands looking through something and John just had to sigh with relief. Barely back, and barely healed and she was already going back to work. To get her attention he cleared his throat which caused her to look up.

"John," She stated with some surprise. "what are you doing here?"

"Seeing you."

Elizabeth gave him a small smile. "I know that, but I thought that you and Rodney were looking for a new home."

"Well we are," John confirmed, glad to be slipping back into their usual banter. "in fact we found the most perfect planet with large oceans, nice views..."

"Sounds almost perfect." Elizabeth stated with a wry look on her face. "What's the catch?"

John shrugged as he sat on the edge of her bed. "Some snake like creatures on the mainland, you know the usual welcoming committee for the Pegasus galaxy."

That elicited a laugh from Elizabeth. "Of course..."

An uneasy silence descended upon them and it was John who first broke the silence. "Listen we uh, should probably talk about what you did back there."

"It was no different than what you have done." Elizabeth stated simply thinking back to when the city had been under siege. He had been willing to give up his life for her and Atlantis, and she was willing to do the same for him and their people. "Don't you dare pretend that it was any different."

"It is different." John insisted. "You're not military."

"Oh, so are you saying that because I'm only a civilian I can't take care of my people?"

John shook his head. "That's not what I meant."

"Then what did you mean?" Elizabeth asked coldly.

"I meant that because you're our leader, you're not expendable."

That shocked Elizabeth. "Are you saying that our military personal are expendable? Are you saying that you are?"

"What I'm saying," John corrected, "Is that we can easily get more military personal. I don't like that reality, but it's true..." He paused and glanced down at the infirmary sheet. "...we can't get another Elizabeth."

"You can get another diplomat though." She retorted.

John looked up with open eyes. "Not like you."

She was stunned and glanced down at her laptop to compose herself before speaking. "You know John," Elizabeth began slowly. "I'm still half-replicator."

"I know."

"I'm still a threat."

"I know that too." John confirmed. "Although Rodney says that the little buggers are perfectly harmless now."

"Still," Elizabeth stated. "I'm still a security risk..."

"Elizabeth-"

She cut him off. "John, I am." Elizabeth shook her head and looked away. "It would almost be better if you killed me now."

"No way!" John exclaimed in horror. "We are not doing that."

"It's not your call." Elizabeth snapped.

"The hell it isn't." John retorted angrily, getting a sense of déjà vu. "Elizabeth-"

"John," Elizabeth interrupted softly. "I'm half-replicator."

"But you're still half-human." John pointed out desperately reaching out to take her hand which was clenched in the sheets. "And even if you were ALL replicator, I still wouldn't kill you."

"Even if I was a threat to the city?"

"Especially if you were a threat to the city Elizabeth," John promised, his eyes softening. "The worse threat would be losing you and your leadership so don't even consider asking me to-"

"Okay." Elizabeth interrupted a new found determination in her eyes. "Okay, I'll get through this."

"We." John correct with a smile. "We'll get through this. We're a team, remember?"

Elizabeth smiled. "The dynamic duo."

John laughed and was about to respond when he felt the city fall out of hyperspace. And the next thing he knew was Rodney's tinny voice in his hear telling him to get to the chair room to ease the city down.

"I'll be back." He promised, giving her hand a squeeze before he left.

----sparky----

It was night; they had touched down safely on 'New Lantia' and had contacted the SGC. Samantha and Bill were taking their time saying goodbye in preparations to go back and debrief General Landry and John found himself on the balcony over looking the new sea with two moons.

"There you are." Elizabeth stated with a smile as she came out onto the balcony after being released from the infirmary.

John nodded and gestured to the view. "Two moons."

"Actually," Elizabeth corrected. "Rodney tells me there are five and that it's just these are the only to visible to the naked eye."

"Really?" John asked arching an eyebrow. "He didn't tell me that."

"Guess he likes me better."

"Yeah." John agreed with a smile.

"I hear that Colonel Carter and Rodney got us re-connected to the Intergalactic Bridge."

John smiled. "Yeah, from what I heard they were all very relieved to hear from us..." He turned to look at Elizabeth who was leaning against the railing herself. "...though they are sending someone out here to determine if you're still fit to run this place."

Elizabeth nodded sadly. "I figured that was coming."

"We'll get through this Elizabeth." John promised with a determined look on his face. "No matter what they say, I won't let you go without a fight."

"Thank you," Elizabeth stated overlooking John's 'I' instead of the 'we' that she expected. "But believe me; I have no intention of leaving."

"Well that's a relief." John murmured. "Cause Teyla said that after this crisis you were thinking about stepping down."

"That was then." Elizabeth explained with a shrug of her shoulders. "This is now." She laughed and turned so her back was leaning against the railing. "Everything's going to change now," Elizabeth asked turning to look at John. "Isn't it?"

John nodded. "But when are things NOT changing in the Pegasus Galaxy?"

Elizabeth didn't answer him, she didn't have too. Her smile was enough. She turned to lean her elbows back on the railing and together they stood there in silence over looking the new ocean of their new home. Both of them wondering what tomorrow would bring.

But whatever was on the horizon, at least they were facing it together...

* * *

A/N- Thank you to AtlantisGate, jasminesmommy, sparklyshimmer2010, janib, stargatesomeone, Anne, Traci, Keegan Paige, courtneymundie7, sb4ever and Jenni. Please take the time to review this little drabble as well... 


	3. Part I: Arguments

A/N- In between my ending of Lifeline and Reunion.

**What Would Elizabeth Do? **

Arguments

Elizabeth was sitting in her office, still amazed that it was still unscathed from both the wraith attack and the beating that the whole of Atlantis had taken when John had 'kissed the surface' of the ocean. Elizabeth smiled to herself and tried to focus on the reports before her but she couldn't. The IOA were sending a representative to talk to her and see if she was still up to commanding the expedition.

_I can understand why they're doing this,_ she had told John when he had come to her the night before on their balcony complaining that she had been through enough and that they should just leave her alone. _But John,_ Elizabeth had continued, _we took a risk- I took a risk and now we have to accept our consequences._

_But we almost lost you..._ John had replied, his brow furrowing. _And I would hate to lose you again. _

_You John?_ Elizabeth asked with a flirtatious tone to her voice. _You would hate to lose me again?_

_Uh-_ he was at a loss for words for a moment. _–by 'I' I mean everyone here on Atlantis of course. _

_Of course, _Elizabeth had echoed with a smile. _Of course..._

_Still_ John had continued. _If they do take you away, don't worry- we won't let you go without a fight. I'll make sure of that. _

_Thank you John,_ Elizabeth had whispered, John's vehemence touching her deeply. _That really means a lot. _

And now it was D-Day, the day that she would learn if she would go or stay, if she would be replaced or...

"Hullo Elizabeth."

The voice was familiar, and when Elizabeth looked up a familiar and most welcome face greeted her. "Jack!" She exclaimed with surprise as she stood up and extended her hand. "Hello."

"Hello to you too," Jack stated ignoring her hand as he sat down. "You'll excuse me if I don't shake your hand."

"Jack," Elizabeth chastised admonishingly. "It's me. Elizabeth."

"With little buggers in your blood."

"Those 'little buggers' as you call them are the only things keeping me alive." Elizabeth pointed out as she sat back down. "And for your information I'm not happy about my current situation either..."

"I know that but-"

"But I've come to live with it." Elizabeth interrupted. "And that's the point Jack isn't it? I'm alive and here talking to you..." She paused and placed her arms on her desk. "...why did the IOA send you anyways?"

"They wanted you to talk to a friendly face I guess." Jack stated with a shrug.

"You haven't been so friendly so far."

"It could have been worse." Jack stated with a shrug. "It could have been Woolsey."

Elizabeth laughed half-heartedly at that. "So what's the verdict Jack? Can I stay or no?"

"No."

"What?" Elizabeth asked, her eyes widening. "I can't? Why not?"

"You're a replicator Elizabeth." Jack stated as thought that would explain it all.

"Half." She corrected. "Half replicator."

"Schematics..."

Elizabeth glanced down to her desk trying to compose herself. She of course had been expecting this but still. "What do you mean by 'go' Jack?" She asked looking back up. "Do you mean that I've been replaced?"

"What else would I mean?"

"I don't know," She admitted. "But Jack-"

"You have twenty-four hours to clear out." Jack stated bluntly, causing Elizabeth to stop in shock again. "I'm sorry."

"Twenty-four hours?" She muttered. "You mean I have to leave completely?"

"Yes." Jack confirmed.

"I can understand replacing me as the leader of the expedition but the IOA should want to keep me here as a negotiator at the very least."

"I'm sorry Elizabeth." Jack apologized. "But you have to come back with me."

"I'd like to see you try."

"Excuse me?" Jack asked.

Elizabeth shook her head. "I'm not going anywhere Jack."

"You don't have a choice."

"The hell I don't." Elizabeth argued. "I was forced to leave my home once, I'll be damned if I'm forced to again."

"Elizabeth-"

"Nothing you say will change my mind Jack." Elizabeth interrupted, crossing her arms in front of her chest as she leaned back into her chair. "I am staying: you can take that back to the IOA."

"They could send a couple dozen SG teams." Jack muttered. "Take you by force."

"Again," Elizabeth stated coldly. "I'd like to see them try. My expedition members won't let me go without a fight. Colonel Sheppard will see to that."

"Well Colonel Sheppard doesn't have-"

"What he doesn't have in terms of military protocol," Elizabeth interrupted again. "Is nothing compared to what he does have in loyalty, and honesty and-"  
Jack stood abruptly. "You're not going to change your mind, are you?"

She merely shook her head. "No. I'm not."

"I guess I better tell the IOA then."

"Yes," Elizabeth agreed. "You better."

Jack was halfway out her office when she spoke up again. "Tell them that I'm only refusing to come back to Earth." She explained. "I will step down from my position as leader with no problem. But I will not under any circumstance leave Atlantis. This is my home Jack... how would you feel if you were made to leave YOUR home?"

He paused for a minute before turning to face her. "I'd feel horrible." Jack stated simply. "And for the record I was promoted and forced to leave my home, so I know what you're talking about."


	4. Part I: Changes

A/N- During Reunion, only with Elizabeth.

**What Would Elizabeth Do?**

Changes

John was fuming, he had been fuming since Elizabeth had told him what the IOA had proposed and how she was being forced to step down. _Just be thankful that they're letting me stay_. She had told him. _Be thankful that they're not dragging me out of here. _John had laughed at that. _As if they could have._ He had told her, and he still believed it. He knew that there was no way that anyone would get Elizabeth out of Atlantis ever again. But still as he told Carter about the war that they had started, he couldn't help but want to change subjects completely especially considering what he knew.

"The wraith replicator war is in full swing." He told her. "From what I hear, the replicators are kicking some serious ass in their last offensive."

From Stargate Command Sam smiled. "Well that's good news John. Well done."

Rodney at that moment walked over. "Hey."

"I'll have the reports ready for you." John continued, ignoring Rodney.

"Sam!" Rodney exclaimed upon seeing who John had been talking to. "Uh- what's new?"

"Just making preparations for the change in command here," John stated through gritted teeth. "Seems we'll have someone else in control in a couple days..."

"Oh you don't have to tell me." Rodney stated with a smile. "I already know."

"Really?" Sam asked, tilting her head to one side.

"I just wanna say that I think the IOA could not have made a better choice."

Sam was touched. "Thanks Rodney."

"Oh don't thank him." Elizabeth interrupted coming up to John's other side. "He thought that he was getting my chair."

"What you mean-?"

John shook his head at Rodney's stupidity. "She's our new boss."

"Oh," Rodney muttered with a roll of his eyes as he stalked away.

"Do you think he'll ever forgive me?" Sam asked the two of them.

"I don't know about that." Elizabeth stated with a smile. She was genuinely glad that it was Sam taking her place as the leader of the expedition- even if it meant that one of her people had been passed over. "But I think that he will..."

"Well I'm just glad that the IOA agreed to let you stay on as a consultant." Sam continued. "I'm going to need all the help I can get."

"Well we're both here for you." John muttered through gritted teeth. "So don't worry about it."

---sparky---

The change of command was taking place; Carter had just stepped through the gate to face the members of the expedition. She wanted to address them but first Elizabeth stepped forwards.

"Now I know that the past few weeks have been stressful for you all," She began looking at each member. "and I know that a change of command is the last thing that you want right now. But I want you all to know that this is for the betterment of us all, and I'm not going anywhere. Atlantis is my home, and you all are my family and I will be here with you all..." There was a murmur that ran through the crowd and Elizabeth knew that she had to wrap things up. "...and while this change may be difficult I want you all to give Colonel Carter your utmost respect and patience. Bestow upon her what you have bestowed upon me, your support, your loyalty and most importantly your trust...that is all."

Then Carter spoke. Elizabeth was a hard act to follow but she somehow managed to say what she had wanted to say and both Elizabeth and John had complimented her on it.

"Do you want a tour?" Rodney had asked with an expectant smile but Sam just waved him away muttering something about wanting to find her way around on her own.

---sparky---

There was a knock on her doorway and when she opened it Elizabeth was shocked to see Ronan standing there. "Ronan," she stated standing out of the way to let him come in. "What can I do for you?"

"You can talk to Colonel Carter." Ronan said curtly. "That's what you can do."

"What's wrong?"

"I found some of my people and I wanted to bring them back here but-"

"But the IOA has new rules." Elizabeth interrupted with a knowing sigh. "There's nothing I can do Ronan, I'm pushing things as it is."

"But-"

"What would happen if the wraith or the replicators found out that we were here?"

Ronan shook his head. "My people wouldn't tell."

"All people talk," Elizabeth argued. "Tongue's slip, mistakes are made. Even you can't guarantee that they won't say anything."

Ronan knew that she was right, and had nothing to say to that. So he merely nodded and turned to leave- muttering something about being sorry for bothering her.

---sparky---

"Elizabeth." Ronan was shocked, he wasn't expected to see her in his quarters. 'What are you doing here?"

"I came to see how you were doing." She stated nodding to the suitcases. "You're packing."

"Yeah."

"I know that nothing I say is going to stop you." Elizabeth began with a sigh. "But I do hope that you'll reconsider..."

"There's nothing to reconsider."

"Ronan, please." Elizabeth stated her voice wavering slightly. "I don't understand why you would want to leave not after thanking me for letting you stay."

That stopped Ronan in his tracks. "You heard that?"

Elizabeth nodded. "Yes, I did."

"I uh- I didn't know."

"I didn't think that you did." Elizabeth said. "Or else you wouldn't be packing now..." Ronan didn't say anything and Elizabeth knew that she would have to chance tactics. "Just stop packing until you guys get back from the mission okay?"

Ronan nodded. "Okay."

---sparky---

"I'm sure you did everything you could." Elizabeth comforted as Ronan was being treated for a burn on his arm. "But please let the doctor to his work."

"I said I'm fine..." Ronan snapped before continuing on. "I tried to radio Sheppard but got no response from him, Teyla or McKay."

"And what about the Satedans?" Elizabeth asked curiously.

"We got separated. I'm guessing the Wraith got to them too."

"So much for this being a cakewalk." Elizabeth muttered, fear rising in her chest; once again John and his team had gotten into trouble, and Elizabeth was just praying that they would be alright.

Sam sighed. "Okay, we've gone from support to rescue and recovery." She turned to Elizabeth. "Get Dr. Zelenka to ready a jumper."

"They'll be expecting us." Ronan pointed out.

Sam nodded and turned back to Elizabeth. "Make that two jumpers Dr. Weir."

"I understand."

---sparky---

Elizabeth was standing back in the control room, back in control- for the moment.

"Dr. Weir." Sam stated through her radio from the puddle jumper. "This is jumper one ready to go."

"Jumper one," Elizabeth replied. "You have a go." And as the jumper disappeared from sight Elizabeth closed her eyes and enjoyed the feeling of being in control once more- even if was during such a horrid and stressful time.

---sparky---

Another remnant of his of his home was gone, and as Elizabeth looked over the balcony and Atlantis she couldn't help but feel sorry for him. When the doors behind her whooshed open she didn't need to turn to see who it was, who else would be coming to see her.

"Dr. Weir?"

Elizabeth turned with a forced smile on her face. "Colonel Carter, what can I do for you?"

"Well you can start by calling me Sam."

"Alright Sam, but you have to call me Elizabeth" Elizabeth agreed and Sam nodded. "What can I do for you?"

"Forgive me for one thing."

Elizabeth was confused. "What do you mean?"

"Taking your job." Sam stated simply. "I took your job."

"It could have been someone else." Elizabeth stated with a smile. "It could have been someone worse. It could have been Rodney."

"His name was on the short list." Sam stated with a small smile as she joined the former leader of Atlantis. "As was John's."

"They actually considered him?" Elizabeth asked with surprise. "I wouldn't have thought that- well, with everything..."

"He's proven what he's made of." Sam stated simply leaning on the railing. "He's grown beyond the Major that was stuck in Antarctica..." She paused and turned to Elizabeth. "...that's thanks to you, you know."

"Oh I don't know about that."

"You shouldn't be so modest Elizabeth." Sam stated. "A lot of people have grown under your command. I mean take Rodney as an example."

Elizabeth laughed. "Yes, Rodney has become more brave in the past four years."

"And more honest," Sam agreed. "Although his ego still gets in the way..."

"Well he wouldn't be Rodney with out it."

Sam turned to Elizabeth with a smile. "Did you know that he actually came to tell me that he's seeing someone!?" She laughed as though it was ridiculous. "He actually thought that I still carried a torch for him, as if I ever did in the first place. He's not the sort of person that a girl could love easily."

"No." Elizabeth agreed with a small smile. "But Katie Brown seems to have a place in her heart for him." She turned to look Sam in the face. "And I know that all of us here love Rodney in our own ways."

"Even you?" Sam asked curiously.

Elizabeth nodded. "He's saved my life on more than one occasion and last year when we thought we were going to lose him..." She shook her head and leaned on the railing. "...losing a dear friend is not something that I care to experience again."

"I know what you're talking about." Sam muttered quietly. "I know what you're talking about... I've been there. Far too many times..."

Elizabeth sighed. "The transition isn't going to be easy."

"It never is," Sam pointed out. "Is it?"

"No." Elizabeth agreed. "It's not. But you have me. I'll be here to help you, talk my people down from the wall if need be."

Sam stood up abruptly. "I can take care of things myself Elizabeth."

"I wasn't saying that you couldn't."

Sam sighed and leaned against the railing again. "I really didn't want this post you know; I have a life back on Earth. SG1- they're my family and leaving them was so hard..." She shook her head. "...I guess I understand why you forced the IOA to let you stay. I just wish that I could have done the same. This isn't going to be easy for me."

"Change is never easy." Elizabeth stated placing a friendly hand on Sam's shoulder. "But it happens all the time." Elizabeth turned to go but stopped and said one more thing over her shoulder. "Welcome to Atlantis Sam."


	5. Part I: Within Dreams

A/N- Aside from Kate dying, and Lizzie not being a part of the episode- I was actually most impressed with Doppelganger, surprisingly. As always, some dialogue is mine, some is not. Oh and as always, thank you to you lovely sparky readers who have reviewed my work. Please review this chapter too if you can...

Within Dreams

Jennifer turned to John. "All your scans are clear, blood tests are normal..." She shook her head. "As far as I can tell, you're in perfect health."

"See?" John stated turning to Elizabeth who was biting her thumbnail. "I told you." He smiled and turned to Jennifer. "Thanks Doc."

Jennifer smiled, but pointed at John sternly. "No more touching strange things."

"That's good advice." Elizabeth stated with a smile. "Thank you Jennifer."

"You're welcome Elizabeth." Jennifer replied.

"I don't know about you..." John began as he jumped off the infirmary bed. "But I am exhausted."

"You've had a long day." Elizabeth agreed.

"Well, thanks for hangin' out."

Elizabeth just lowered her gaze and shook her head. "I wanted to make sure that you were alright." She raised her gaze and looked up at him as they walked. "I mean considering you touched an alien identity you were remarkably lucky."

"I'll say." John agreed as they rounded a corner and came across Teyla.

"I was just coming to see if you-"

"He's fine." Elizabeth stated but Teyla gave John a suspicious look.

"I'm fine." He insisted. "Really..." John smiled and bowed his head slightly. "But if you will excuse me ladies, I'm tired. I'll see you both tomorrow."

And with that John walked passed Teyla brushing her shoulder as he passed by. Niether she nor Elizabeth nor John noticed the eerie white glow that had followed.

--sparky--

Lorne had John cornered in a hallway/landing of Atlantis. "Put down the gun Major," John ordered his hands up in the air. "Let's talk this out."

"Someone get an A.R.G. Now! Shoot him with it?"

"Lorne?" Elizabeth asked walking down the stairs. "What are you doing?"

"Don't you come any closer." Lorne stuttered pointing the gun at Elizabeth briefly. "You're a replicator too."

"Half." John corrected sternly causing Lorne to turn his attention back onto him. "She's half replicator, but we know this."

"Okay," Lorne rationalized. "But that doesn't mean that you're not one." He looked around frantically. "Someone just shoot him! What's the harm? I-I-if he's human, it won't hurt him. Right?"

"John?" Elizabeth asked curiously. "What is he talking about?"

"Don't talk to him Dr. Weir!" Lorne ordered. "He's a REPLICATOR!"

John frowned. "Look Lorne, I don't know what's gotten into you but-"

"Oh it's not me." Lorne countered. "It's not me."

"Major," Sam stated as she arrived on the scene. "How 'bout you lower your weapon?"

Lorne just looked at Sam as though she was crazy. "He's a replicator!" He received no response from Sam so he continued. "What, you don't believe me? Okay, I'll shoot him, you'll see."

"You'll do no such thing Lorne." Elizabeth stated angrily stepping squarely in front of John. "He hasn't done anything."

"Call for an ARG."

John just turned to Sam in shock. "You believe him?"

"No," She whispered back to him quietly. "But it won't hurt you, and it might help him to lower his gun."

"You're one of them too." Lorne accused. "Everyone knows that a replicator was made of you- you have to be her and the real Colonel Carter is back at the SGC right now and-"

"Lorne,"

"And she's been compromised." Lorne stuttered as Elizabeth took a step forward. Lorne kept his gun trained on Elizabeth and turned to the marines that were surrounding him. "Well, don't just stand there. Shoot them! Shoot the three of them, it's a replicator take over."

"Now listen here Lorne," John began coming to stand beside Elizabeth but he froze when Lorne aimed his gun prepared to fire. Just then a blast of red energy hit Lorne and he crumpled to the floor. They all looked up and saw Ronan putting his own weapon away. Things were quickly spiralling out of control.

--sparky--

Things quickly spiralled from bad to worse. Kate Hieghtmeyer died and the entity had transferred to Elizabeth. _I thought that because I'm half machine that I'd be immune!_ She had pointed out when they had put her in isolation for the protection of the rest of the city. _We thought so too._ Rodney had agreed. _But clearly because you have conductive material within you now..._ He hadn't needed to say anymore. Elizabeth was the perfect incubator for the entity. And now, they had to get it out.

Volunteering John agreed to be hooked up to Elizabeth via a piece of technology that the SGC had encountered years before. And while John was a little hesitant about going into her dreams, he was damned if he was going to let her die on him again.

_You don't have to do this you know._ She had told him, moments before she had been put under. _You really don't._ John had just shaken his head at that. _It's my idea,_ He had told her. _And beside, Carter accused me of thinking of you, might as well get inside your head to see if that's really true or not..._

And that's how he found himself within her dream. He was standing in the control room which was in chaos. It was clear that the city was under attack and he could see that the expedition members were losing.

"McKay!" Elizabeth barked as she sent more people through the gate. "We need the shield up! We're losing people!"

"I'm sorry Elizabeth. But Rodney's not going to answer."

Confused, Elizabeth turned to see John standing before her. "John?" She asked tentatively. "What are you talking about?"

"I'm talking about how you've failed everyone." He stated simply. "The city is falling because of you. You led the replicators right to our doorstep."

"I thought you were here to help." Elizabeth stated in horror as she backed up, running right into another body.

"Don't listen to him." John, the real John ordered. "He's not real. He's the entity."

Elizabeth turned to see John, her John standing there and she remembered what they were trying to do. Whirling back around the creature she let all her fear go. "Leave me." She ordered. "Leave me and you can go home."

The evil non-real John laughed. "I am home."

"Don't give up Elizabeth." John encouraged.

"Don't give up Elizabeth." The fake John mocked. "You have to give up, you won't be able to survive."

"I will always survive." Elizabeth countered sternly as she glared at the machine. "I have survived everything that the Pegasus Galaxy has thrown at me and I will survive you. You can NOT hurt me."

"Wanna bet?" The evil John taunted. The real John and Elizabeth just looked at him as they felt the city shudder beneath their feet and explode all around them.

--sparky--

John suddenly opened his eyes and turned to face Elizabeth. "What happened?"

"Clear!" Jennifer ordered as she shocked Elizabeth with the defibrillator.

"She's in cardiac arrest." Rodney answered as he pumped air into Elizabeth. Again and again Elizabeth was shocked but soon the dead-pan monotone beep filled his ears and he knew that she was gone.

"I'm sorry," Jennifer whispered sadly. "I've done all I can. We've lost her."

John was in utter shock, Elizabeth was dead. He looked up at the observation room into the eyes of his friends and found that they were all hard and cold. Knowing that he could do nothing he left the isolation room and wandered aimlessly through the halls of Atlantis; until he came across an image of himself.

"You killed her you know." His doppelganger stated. "You failed her. You've always failed her."

"Bastard." John muttered full of rage as he hurled himself at the monster before him.

--sparky--

"What do you mean the entity is in him?" Elizabeth asked worriedly as she sat up. "What happened?"

"You went into cardiac arrest Elizabeth." Rodney answered. "And when Dr. Keller shocked you, the entity jumped ship."

"So it's afraid of electricity." Elizabeth concluded watching as Rodney mutely nodded. She looked past the scientist and at John. She could see his eyes moving rapidly behind his closed eyelids and she knew that she had to help him, like John had helped her so many times before. "Hook me back up."

--sparky--

"I'm not afraid of you." John stated as he and his doppelganger fought in the empty control room. "So why don't you just leave?"

"You are afraid of me." The evil John corrected. "I am the one thing that you ARE afraid of! You've failed your friends. You brought this upon them and there is NOTHING you can do to stop it."

The doppelganger continued to beat the crap out of John until the real John had nothing left to fight back with. He was beginning to doubt himself, and could feel that the doppelganger was gaining strength.

"Fight you coward." The doppelganger taunted. "FIGHT!"

John groaned and shook his head. "No. That's what you want."

"It's your fault Heightmeyer's dead." He sneered. "It's your fault that your precious Elizabeth it dead."

"I'm not dead."

Both John and the doppelganger turned in surprise and saw Elizabeth walking smugly down the stairs. Before either John or Elizabeth could act the doppelganger had her pinned against the wall. Elizabeth grimaced in pain as the doppelganger gripped her throat like the real John had done two years previous.

"You can't win."

"Yes we can." Elizabeth wheezed, quickly losing her breath. "You're vulnerable to electric shock. That's why you couldn't kill me." And as soon as those words were spoken, bolts of electricity zoomed in from practically nowhere and attacked the alien creature until it fell to the floor. Elizabeth put her hand to her neck while John, gathering all the strength he could muster- tossed the doppelganger through the gate which promptly shut down.

"Is it over?" John asked turning to Elizabeth who looked slightly off balance.

"I hope so." She answered sincerely as John helped her to find her balance by holding onto her shoulders. "You are you right?"

"Yeah." John confirmed with a nod of his head. "And you are-"  
"Me." Elizabeth stated. "Alive."

"That's good to know." John said.

Elizabeth smiled. "So this is your dream world?"

John nodded. "Yeah, didn't know that Atlantis was so much a part of my psyche."

"I know what you mean." Elizabeth agreed when suddenly a thought struck her. She looked into John's eyes and took a deep breath.

"Are you okay?" He asked concerned.

She merely nodded and ignored the question. "I know that this is just a dream, and technically it's not real but I need to do this now when I have the guts to do it."

And before John could say anything Elizabeth placed her hands at the side of his head and pulled him in for a kiss. Their lips locked and John instantly felt as through he was home. Although that feeling vanished in an instant as he jolted awake.

--sparky--

It was later that night in the mess hall when Elizabeth walked in to find John still awake going through reports. Not saying a word she simply sat down with her coffee and shared a smile with him. She knew as well as he did that that what had transpired in the dreams was remembered—and while she would have liked to have spoken about her actions, Rodney ruined it by joining them with a huge plate of fruit. They were then joined by Teyla, and Ronan, and Lorne and Zelenka and Jennifer and Keller. And as the team joked the night away, Elizabeth took a couple stolen glances towards her former second in command and new that within a dream an entire world had opened up for them.


	6. Part I: Out in the Universe

A/N- So Travellers was another lack lustre episode from our dear powers that be and although it had its moments, they were few and far between. And I don't know about anyone else but the fact that John was kirking it up after a whole season of being not kirk well, was unnecessary really. And what was with the closet? That's been a thing of sparkies since like the inception of Atlantis on television and what do the powers that be do? Put John in a closet with a hot looking alien chick. -- (sigh) What can we do really other than read and write fanfiction. The high point of the episode though? No Carter although in MY version within the canon structure, she's needed. (Sorry 'bout the lateness of this too I mean school is totally hectic right now)

Out in the Universe 

Somehow, there isn't enough time to talk about what really matters. And although they had plenty of opportunities to bring it up neither Elizabeth nor John talked about what had transpired in his dream world. It was their only little secret and deep down both of them were afraid that if they talked about it, they would ruin that magic moment that they had shared.

But after weeks of avoiding it Elizabeth was determined to talk to John about it. She was not one to run from a discussion and she was damned if she was going let them continue on as though nothing had happened.

That was why she was in the control room with Rodney, listening as the two friends bantered back and forth with each other.

"Atlantis this is Sheppard, I'm on approach to the gate" John stated, taking a bite of an apple.

"Acknowledged, you know since I've been in Pegasus I have set up like what- half a dozen research stations on various planets and I don't remember you ever volunteering to run a re-supply mission to any of them"

"I'm a busy man Rodney" "Just happened to have a little free time" bit apple

"And Doctor Mackenzie just happens to be studying a primitive tribe that lives in a tropical paradise and has-how did he put it 'little or no social inhibitions'"

"Now Rodney," John began smiling. "They are a very friendly people and-" suddenly the jumper was hit by something. "What the hell?"

Elizabeth chose this time to interrupt. "John, what is it?"

"Elizabeth, you're there?"

"Yes." Elizabeth replied. "But what is going on there?"

Calling up the heads-up display John stated what he had deduced so far. "I think that someone just took a shot at me. I've got a contact on my H.U.D and they're closing in fast."

"Oh no," Rodney muttered more to himself then to anyone else. "Was it the wraith?"

"I don't think so but-" the jumper was hit again and John changed his sentence. "Whatever they're shooting me with, just shorted out my systems. I can't get weapons online."

There was annoyance and a little worry in John's voice which in turn worried Rodney and through the comm link Rodney could hear the ship being shot at. "Can you make it back to the gate?" he asked worriedly, hoping for a reply but there was none. "Sheppard? Sheppard?" Rodney asked but once again there was no reply. "Crap."

"John?" Elizabeth asked, her voice quivering slightly. "John are you still there?"

There was no answer of course and Rodney was already motioning to Chuck to put him city wide. "Colonel Carter to the control room immediately," Rodney stated his voice rising in panic slightly. "Colonel Carter to the control room..."

Within moments, the new official leader of Atlantis was there. "Rodney what is it?" She asked worriedly as she and Teyla ran up the stairs. Yet before Rodney could get a word out Sam knew what the problem was. She could see it on Elizabeth's face. The worry, the concern and another emotion that Sam knew she had worn on her own face more than once. "It's John." She stated simply, eliciting a nod from Elizabeth. Sam sighed and shook her head. John had just as bad a habit of getting himself into trouble as SG1 had. "What happened?"

Once the situation was explained, Carter created a plan. "Rodney, gather Major Lorne and the rest of your team and check out John's last known location. Maybe whoever shot at him caused him to land on the planet. The jumper could be broken and he is unable to contact us."

Without saying a word Rodney nodded and left with Teyla to collect Lorne and Ronan. Elizabeth meanwhile turned to Carter with a determined look on her face. "I'm going with them." She stated. It wasn't a request it was a statement, an order.

"My office." Sam stated harshly and Elizabeth winced as she walked over the catwalk platform into what up until a little while ago had been her office. "Elizabeth-"

"Colonel Carter, I need to go on that mission."

"I know that." Sam began a little more gently. "But you can't. I'm sorry."

"And why not?" Elizabeth asked, crossing her arms in front of her chest.

"Because if it was the replicators that shot him down then they may still be in the area and then you may be at risk."

Elizabeth wasn't buying that answer. "There's no evidence of that."

"Not yet." Sam agreed. "That's why Rodney and his team are going through first. If all goes well then maybe..."

"I want to go through now." Elizabeth restated coldly. "And you know that there's nothing you could do to stop me."

"Don't threaten me Elizabeth." Sam answered harshly as she too crossed her arms in front of her chest. "I know what you're going through. I've been in this kind of situation more times than I can count and I know that the best thing right now is for our decisions not to be ruled by our emotions."

"Our emotions?" Elizabeth asked, her heart stopping slightly. "What are you-"

"Don't play dumb." Carter stated her voice dropping to a whisper. "You're above that Elizabeth."

There was a moment of silence before Elizabeth spoke again. "I don't understand."

"I don't know if you ever will." Sam responded, her voice softening with understanding. "God knows that I never did." It was that sentence that caused Elizabeth to look up and she remembered the look in her eyes when she had told SG1 that they might have to wake up O'Neill from his frozen sleep in Antarctica.

'She knows.' Elizabeth thought in horror, realising that all this time her emotions had been dangerously close to the surface. 'I think she's always known.' She took a deep breath and confronted the new leader of Atlantis. "So we wait then?"

Sam nodded. "We wait. If the area is secure then maybe you can go but until then..."

Elizabeth nodded as Sam trailed off. She muttered a small 'thanks anyways' and made her way out of the office and into the control room. _John's always getting himself into trouble_ she thought worriedly to herself. _I can't only hope that he manages to stay out of anything really serious and comes back...we has to have a very long talk about everything. _

---SPARKY----

Rodney and the gang came back disappointed. There was no next step to be had. There was no way to trace him and while no one was willing to believe that, it was Elizabeth who was willing to take the risk.

"Listen to me," she argued. "If the replicators did take him then I'm his only hope."

"You can't risk it Elizabeth." Rodney argued over the conference room table. "Sheppard wouldn't want you to risk it. Not again."

"But it's my risk to make isn't it?" Elizabeth asked looking from Rodney to Carter to Teyla, Ronan and Keller. "It's not that hard, you drop me off on the planet, I cast out my senses and see what I can find."

"No." Sam stated her hand clasped in front of her. "I'm sorry. But I can't let you do that. It poses too much of a risk to both yourself and Atlantis."

"But I'm still a risk just sitting here aren't I?" Elizabeth asked angrily, her rage and worry barely being contained. "What do you expect me to-"

"Elizabeth," Rodney interrupted. "We've already been over this. Your nanites pose no threat."

"Other than the fact that I'm still half-replicator."

"Yes." Rodney agreed. "Other than that,"

"So let me put that side of me to good use." Elizabeth stated, beseeching Sam to change her mind. "Please."

"Elizabeth," Teyla began slowly. "What if it is not the replicators that took John? What if it was someone else?"

"But if wasn't the wraith and it wasn't the replicators," Jennifer began voicing what everyone was thinking. "Then who was it?"

---SPARKY----

Somehow, someway Rodney had been proven wrong and excitedly he called Ronan, Teyla and Elizabeth down to his lab. "Rodney," Elizabeth began as soon as she walked through the door. "Tell us that you've got good news."

"Oh better than good." Rodney stated with a smirk. "Do you remember how I said that sometimes there was nothing we can do? Well, I'm right about that- but not this time."

"You found him." Elizabeth stated, relief washing over her. "Where is he."

"Well, it's more like he found us. Listen to this." Rodney typed on another laptop and white noise came flooding through only it was punctuated by an occasional random fluctuation. "Now that is the sound of sub space-" Rodney began, rambling on about how white noise is generated by radiation but who the ancients managed to create a program that could sense artificial patterns. "It's no doubt a long-range means of detecting-"

"Rodney." Elizabeth interrupted. "The point?"

"Oh, I uh- picked up this." He typed some more and a new more regulated sound came through the speakers.

"What is it?" Teyla asked looking intrigued.

"That, is Sheppard." Rodney stated proudly. "Now I-"

"And how do you know it's him?" Ronan asked interrupting Rodney himself.

"It's-"

"It's morse code." Elizabeth finished her eyes lighting up. "S.O.S"

"Exactly." Rodney stated with a smile. "With it, we can find him."

---SPARKY----

They flew through the space gate but soon realised that it would take them five hours to find John. Settling down in her seat Elizabeth glanced back briefly to Rodney and Teyla who were sitting in the seats and Ronan who was standing in the doorway. They had a long wait in front of them, and Elizabeth wasn't sure if her already frayed nerves could handle much more.

---SPARKY----

Rodney was getting frustrated. Not only were the ships too far out but he had no answers. "How should I know?!?" He asked Lorne angrily. "We don't even know who they are remember?"

"Does it really make a difference?" Elizabeth asked, quelling the argument between the two boys. "Even if it was a fleet of hive ships, or Aurora class vessels, would it really stop us from trying to get him back?"

Her question hung in the air until someone spoke up. "No." Ronan stated standing in between Teyla and Rodney. "It wouldn't."

"No." Lorne agreed. "It wouldn't."

---SPARKY----

Of course, what ever powers that ran their universe were looking out for them all and even though the ships disappeared off their sensors soon after coming within weapons range. John appeared in the jumper safe and sound, and back on Atlantis he plus his team were sitting at a table in the Mess Hall enjoying a meal.

"This is really good."

Rodney scowled. "Really?"

John nodded. "Mmmm. You spend enough time with a bunch of space nomads, you really begin to appreciate what you have."

"It is difficult to imagine spending one's entire life on board a ship." Teyla stated.

"If it was me," Ronan began waving his fork around. "I'd go crazy."

"Well they're not exactly the most even-kneeled people out there and I'm still not sure why they let me go." John stated with a shrug.

"Still, you offered them an alliance." Elizabeth piped up causing John to look at her. "Maybe that was worth something. It has to be considering all we can offer."

"Not that I told them really." John stated with a smile.

"They could have figured out that you'd be more trouble than you're worth." Ronan suggested, eliciting a laugh from John.

"That is a distinct possibility."

"No." Rodney mused suspiciously. "There's something you're not telling us." When John took another bite of his food, Rodney knew what was going. "She was hot, wasn't she?"

John could feel Elizabeth's gaze upon him and decided to go for the middle path. "I don't know what you're talking about."

"Oh," Rodney began furious. "I knew it! That is so typical. You are such a Kirk"

"She had me beat Rodney." John pointed out, trying to set the record straight. "And she threatened to kill me several times. It wasn't like we were hanging out in the spa together."

"Still," Rodney began angrily. "All I know is that every single time that I've been taken captive it's been with the wraith. Just once, only once would I like to be taken prisoner by the sexy female alien."

John smiled shaking his head. "You may still get a chance."

"What do you mean?" Elizabeth asked, eyeing John carefully.

"She's still out there."

And while, Rodney looked hopeful Elizabeth studied John. _Clearly,_ she decided finally. _He's still too much of a Kirk to tell him anything. I can't tell him anything. I'll just have to wait._


	7. Part I: Remember Me

A/N- In terms of 'Tabula Rasa' I actually liked it. I mean it was hardly anything without our dear Lizzie but it had its moments.

Remember Me

Everything was falling apart. And while Elizabeth stalked through the city trying to keep herself safe she couldn't help but wish that she was at least going through this experience with her people. 'Just one more thing to chalk up to my being different' she told herself as she tried to escape the wandering soldiers. 'But I have to try and find Teyla she-'

Suddenly there were noises and she could see Zelenka and Rodney talking to each other. They were still to far for her make out the words but as soon as she took a step they split up. 'Damit.' She thought angrily to herself. 'If only I had gone with John and Ronan...'

---SPARKY----

The hours passed, but Elizabeth just couldn't make it to the brig. She knew that that was the most likely location that they would be holding Teyla. But every time she got close, the soldiers would shoot at her...and of course she would have to lose them every time. _In case it gets really bad,_ he had told her before he left. _Don't hesitate to shoot. _

_I am not going to shoot our own people John._ Elizabeth had told him firmly. _Not matter what it comes down too_.

'But now I think I have no choice.' She thought forlornly to herself. 'I'm running out of options.'

---SPARKY----

Elizabeth was no scientist but she knew that time was running out. And to make matters worse, she had been dragged to the jumper bay by Lorne's men. _We can't take a chance on taking her to the brig_. They had decided. _She has to come with us._ And now Elizabeth was waiting with them to see who would come out of the jumper.

"Hands in the air now," Kemp one of the men in front stated as John and Ronan exited the jumper.

"Listen, Lieutenant." Ronan began slowly. "This is medicine. We need to deliver it."

"Lt. Kemp," Elizabeth began piping up. "Listen to them please."

"Dr. Weir?" Ronan asked looking to see Elizabeth pushed in front of the soldiers to stand with John and Ronan. "I thought-"

"I know." Elizabeth stated with a sigh as she too put her hands up in the air. "But things didn't exactly work as we planned."

"Let's take them to the brig." Lt. Kemp spoke up causing Ronan to groan in frustration.

"You're making a mistake. There are sick people who-"

'What the hell is going on here?" Lorne asked entering the room.

"Sir," Kemp began. "We caught these men trying to infiltrate the base.

"And the woman?" Lorne asked indicating to Elizabeth.

"She must have helped them sir." Kemp began, not noticing that John was now noticing Elizabeth for the first time- or so he thought.

"Hey," he stated with a dreamy look on his face as he looked past Ronan to her. "You're really cute."

"What?" Elizabeth asked turning to John in surprise. "What did you say?"

"I said-"

"Quiet." Lorne ordered.

"Lorne," Ronan interrupted, putting John's comment out of his mind. "You've got to listen to me. Everyone on this base is going to die if you don't."

"And who are you exactly?"

Ronan sighed. "Look in your pocket."

"What?"

"Look in your pocket Major." Elizabeth stated not believing that she had forgotten that the picture was in there. "It will explain everything."

---SPARKY----

It was a day later, the anecdote had been distributed and while Ronan and Teyla were taking some much deserved rest, Elizabeth found herself waiting at John's bedside.

"Elizabeth," Keller began quietly coming over to her. "You should get some rest."

"I'm half replicator." Elizabeth pointed out with a weary grin. "Don't need that much sleep remember."

"But you do need some." Keller argued. "Now please."

Elizabeth shook her head turning her attention back to John. "No." she stated firmly. "No, I won't leave him. Not again."

"Alright." Keller agreed with a sigh as she left them alone.

'Come on John," Elizabeth prayed as she clasped her hands together. 'You have to pull through.'

Suddenly there was rustling and Elizabeth looked up to see him waking up. "John," she stated with a relieved smile. "You're awake."

"Yeah," he stated drowsily. "What happened?"

"Teyla and I managed to distribute the plant in the ventilation system." She explained, helping him to sit up slightly. "It knocked you out."

"How long have I been asleep?" he asked blinking his eyes a couple of times.

"About a day," she answered honestly.

"A day?" John asked not believing it. "A day?"

"It hit some people harder than others." Elizabeth stated with a sigh as she sat tentatively on the edge of his bed so that she was facing him. "How are you feeling John? How's your memory?"

John sighed. "Well, pretty good I think. I mean things are a little fuzzy, especially the last couple days but if I forget your birthday in a couple weeks..."

Elizabeth smiled. "At least you know that it's in a couple weeks John and if you forget I will forgive you." She sighed and tentatively took his hand. "I'm just glad that you're awake."

"Yeah," John stated, doing his best to ignore her hand on his. "Why do I get the distinct feeling that we almost ran out the clock on this one?"

"Because you almost did," Keller stated coming over, noticing when Elizabeth took her hand away from John's. "If the distribution of the cure had been delayed any longer, many more people would have died."

John just closed his eyes before opening them again. "Ronan, Teyla and Rodney-"

Elizabeth smiled and put up a hand to silence him. "Ronan and Teyla were immune, like me only not like me because-"

"Because you're half replicator," John interrupted with a nod of understanding. "Can't McKay use that EMP thing on you?"

"No." Elizabeth stated sadly. "It would kill the nanites, but because the nanites make up half of me..."

"You'd die too." John finished understanding. "Right; Elizabeth dying, not a good thing, would not have wanted that."

"No." Elizabeth agreed with a small smile. "We wouldn't have wanted that at all."

"But what about Rodney?" John asked worriedly. "He's okay, isn't he?"

"He's with Katie Brown." Keller stated. "She took it harder than most."

"Will she be okay?" Elizabeth asked turning to Keller.

"Hopefully," She answered honestly. "But she was exposed to it longest out of everyone who has survived thus far. But I have hopes that Rodney won't let her go that easily."

"No," John agreed looking from Keller to Elizabeth. "We don't let the ones that we care about leave us with out a fight."

"No," Elizabeth stated, in full agreement with John. "We don't."


	8. Part I: Sight Beyond

A/N- So I'm skipping Missing because that deals with Teyla and her arc. So here I am skipping to 'The Seer' which was an alright episode- despite being a rehash.

Sight Beyond

It's amazing how time does not let you do the things that you wish to do. And as Elizabeth stood on the balcony of the control room watching her friends go through the gate she couldn't help but wish that she had been the one to formally send them off. 'Teyla's people are missing and hopefully she'll find what she's looking for.' She sighed, she aside from Keller knew Teyla's situation and the former leader of Atlantis felt for her friend. 'I can't imagine having the one you love, the father of your baby ripped away like that, if I ever-'

Elizabeth could hardly finish the sentence in her mind, images of John going to his death during the siege of Atlantis and being fed upon by a wraith in front of her flitted to the surface of her mind. While she had ever been intimate with John, she knew now that she loved him, but somehow could not find the words to tell him. 'I'd probably scare him off,' she thought finally as the gate shut off. 'And I need him as one of my dearest friends more than anything...'

Suddenly, _Incoming wormhole_- Chuck's voice resounded throughout the city comm. and Elizabeth could see Sam walking towards the gate, meeting Richard Woolsey as he stepped on through. 'Oh great,' she thought forlornly to herself as she saw Woolsey take a look at her and grimace. 'I'm going to get the third degree again.' But then the gate activated again, and Elizabeth sighed with semi-relief as she realised that she was not the prompting of Woolsey's visit.

---SPARKY----

"While you were gone," Sam began with everyone, including Elizabeth being seated in the conference room. "We received a report that the people of M2R-441 were recently visited by a wraith," she paused and turned to John. "Now, from the description of his facial markings it sounds a lot like the wraith who helped you escape from the Genii last year."

"My old buddy?" John asked; his tone unassuming.

Sam nodded. "Apparently, he has a matter of great importance that he wants to discuss with you. We already sent an advance team to the address that he proposed for the rendezvous and the interesting thing is, is that it sounds an awful lot like the planet in McKay's vision."

"So we're believing this now?" Ronan asked suspiciously.

"Davos did know that we were coming." Teyla pointed out.

"And there have been instances of this before." Elizabeth stated turning to Carter. "Something like this happened at the SGC before; with Jonas Quinn- am I right."

"Yes." Sam agreed with a nod of her head. "And believe me, before I didn't believe in visions- but now I'm not so sure." She sighed and turned to Teyla. "Did you ask him about the Athosians?"

The conversation continued, and in the end it was decided that John and his team would go through the gate to meet the wraith. When Elizabeth brought up the possibility of her going, John agreed but Woolsey didn't and seeing how Rodney's vision just had the field team it was decided by Carter that Elizabeth should stay behind. _To keep the $peace_. She had told Elizabeth. _Just until Woolsey leaves_.

---SPARKY----

Things were indeed going from bad to worse. The Asurans were now killing entire populations of humans to stop the wraith. And the wraith was now working somewhat with Rodney to try and fix what he had broken. _It's just not fair._ Elizabeth had told John when he had found her on their balcony. _Why do things always go from bad to worse around here?_

_They're going to get worse. _John had stated. _Davos is dying._

_Oh no._ Elizabeth had sighed placing her head in her hands. _That is not good._

_But he wants to share a vision with you. _

_With me?_ Elizabeth had asked, not understanding. _Why?_

_Don't ask me._ John had told her. _I'm just the messenger._

And that was what Elizabeth was doing in the infirmary. They had already received the vision about the wraith ships, and Carter had received one about Atlantis falling and now it was Elizabeth's turn. Davos was struggling to breathe but he beckoned Elizabeth over and took her hand. What she saw shocked her. _Her team was flying in a jumper, the replicators were after them and they shot them all down. Everyone was thrown around like nothing and Elizabeth could sense that they had died- or all would die._ When she came out of the vision, she could see that Davos was struggling to breath and Linara was crying over him as he died.

---SPARKY----

In the end, Atlantis was safe and Woolsey had gone back to Earth and Elizabeth and John were left alone on their balcony.

"Is Sam still thinking about her vision?" Elizabeth asked as she sat on the railing. "The one about Atlantis being destroyed?"

"Yeah." John confirmed. "I told her that even if our imminent doom was tomorrow that was nothing new.

"No," Elizabeth agreed with a smile. "But at least my vision was more straightforward."

John looked at her with surprise. "You got given a vision? What of?"

"Us." Elizabeth stated before realising that she would have to clarify. "I mean all of us, you me, Ronan, Teyla and Rodney. We were in a jumper trying to get away from the replicators and they shot us down. We all died."

John was silent contemplating her words.

"All I know is that I am NOT going off world in a jumper ever again."

"You can't do that." John stated vehemently. "You need to get off this base for your own sanity."

"I can't John." Elizabeth stated sadly. "I'm not going to take that risk. I almost lost everything once... I'm not going to do that again."

Outwardly John protested saying that the future wasn't set in stone but inwardly he agreed. He wasn't about to be put a position where he would have to lose Elizabeth all over again. He just wasn't ready for it. He had almost faced that possibility once, and it had nearly killed him- even though that moment had been fleeting.

"Well," he stated finally, knowing that he would never change her mind. "As long as you think that you are making the right decision."

"I do." She stated honestly. "I do think that that is the right decision."

* * *

A/N- Hey guys. Thank you to all who have been reviewing thus far and thank you to Charmed225, stargatesomeone, Jenni, sparkly, saphire and jasminesmommy for reviewing the last chapter. I hope that you and the rest of my beloved readers will take the time to review this one too.


	9. Part I: Knowing What Is There

A/N- Millers crossing. A good episode all things considering... adding Elizabeth was fun.

Knowing What Is There

They all flew back to Earth as soon as they heard. Rodney's sister was missing, and John, Elizabeth and Rodney all went to earth to find her. Teyla elected to stay behind because of her condition- which none of the boys knew about and Ronan decided to stay behind to keep Teyla company. _Wouldn't know what to do with myself on Earth_. He had told John and Elizabeth honestly. _Not that I don't want to see where you come from. Maybe get all those references that you and Mckay toss back and forth..._

Back in Jeanie's home Rodney explained the situation to Agent Barrett, John and Elizabeth. "I was bouncing some ideas off her." He stated reluctantly.

"What about?" Barrett asked intrigued.

"Well," Rodney began with a sigh. "Before Sheppard's wraith showed up I was trying to perfect my nanite medical program."

"To help me." Elizabeth piped up. "Stop my nanites."

"Yeah," Rodney confirmed. "It was to be a better and more complex version but as soon as we found out that the replicators were attacking human worlds throughout the Pegasus galaxy we obviously switched our focus to shutting them down once and for all."

"And you sent Jeanie the program that you were working on?" Barrett asked. "Was that such a smart idea?"

"I needed a new set of eyes." Rodney defended. "Look, I know now that maybe the Trust or some other Earth-based organisation wanted info on me or about the program but regardless of that, my e-mail and her capture happened too close together _not_ to be connected.

"Sounds like a place to start." Elizabeth stated with a worried look. She fiddled with the suit that she was wearing and as she looked sideways to John she admitted that he was handsome. Unfortunately, her noticing John made her miss most of the conversation.

"Seriously," Rodney was saying. "This could take ten or twelve hours. Just..." he was at a loss for words, and Rodney was never at a loss for words. "...there's nothing you can do here. Just go back to the hotel. I'll call you if I find anything."

---SPARKY----

They were in Vancouver, and therefore all of them, John, Elizabeth and Rodney had had to book a single room for all of them because some big sci-fi convention was taking place in the area. _Just imagine what they all would think if they really knew_. Rodney had whispered to them as the checked in. _They wouldn't know what to do with themselves._

"Poor Rodney." Elizabeth stated as she sat down on one of the double beds, taking her shoes off. "I can't imagine what he's going through right now."

"I know." John agreed, opening the blinds to let in the sun. "But he'll fix this. He always does."

"Still..." Elizabeth stated with a sigh. "We have no idea where she might be."

"Rodney will find her." John restated, realising that the two of them were stalling. "I mean..."

"Listen John," Elizabeth began causing John to falter in his speech. "I think that we need to talk."

"Now?" John asked.

"Now." Elizabeth confirmed with a nod.

"But everything here is...well..." John sighed. "It's what's making things so difficult."

"No more difficult than back home." Elizabeth stated standing up to face him. "And besides..."

"Elizabeth." John stated looking away. "I don't want to have this conversation with you right now."

"No?" She asked curiously, turning his shoulder so that he would look at her. "Then when are we going to have this conversation?"

There was so much subtext between the two of them, and so much of a connection that Elizabeth could almost hear his thoughts. "When it suits you?" she asked almost angrily.

"Yeah." John agreed with a slow nod. "What it suits me... and you too." He stated looking Elizabeth squarely in the eyes. "I don't think that you are ready to have this conversation, no matter what you think."

"Oh I am ready to have this conversation John." Elizabeth stated bitterly. "But I guess I was foolish enough to think that you were."

"Elizabeth..."

But it was too late. Elizabeth had already put her shoes back on and had stalked out of the room. John in the meantime just sat on one of the double beds and put his head in his hands. "What have I done...?"

---SPARKY----

So much happened so quickly; but it was all over now. And back on Atlantis, Elizabeth found John on their balcony. "You know there is something that I haven't yet understood." She stated as she came to stand beside him. "And I won't understand until you explain it to me."

"What?" John asked, not tearing his gaze away from the ocean.

"You talked Wallace into killing himself."

"He wanted to make things right." John stated, telling Elizabeth the same thing that he had told Rodney. "And I wasn't about to let McKay risk his own life."

"The wraith could have used me." Elizabeth stated thinking back to their argument. _I am the only viable option._ Elizabeth had argued after she had heard Rodney ranting. _The wraith can feed on me and I will be okay._

_We don't know that._ John had stated angrily. _He could kill you._

_I'm half replicator John._ Elizabeth had shouted. _He couldn't kill me even if he tried._

_You don't know that. _

_No._ Elizabeth agreed. _I don't know that. But it's worth the risk. _

_I disagree._ John had argued.

_You can disagree all you want John Sheppard,_ Elizabeth countered. _But you can not tell me what to do. I was your commander once._

_But not anymore Elizabeth, _John had answered coldly. _Not anymore._

"The wraith could have used me." Elizabeth restated. "And you wouldn't have had to cross the line."

"I didn't cross the line."

"John, look at me." Elizabeth stated, her voice holding as much authority as it had in the past. Once John was looking at her she continued. "What is with you? You wouldn't let Rodney sacrifice himself that I understand. He is your friend and a member of your team and you need him. But me-? I'm a potential threat that was probably immune and instead-"

"I didn't want to take the chance." John stated angrily. "Not on you. Not again."

"It wasn't your chance to take." Elizabeth argued. "It was mine." She sighed and softened her voice. "We were a team once... we didn't let the other make decisions alone."

"I know." John stated with a sigh. "I know."

"What happened?" Elizabeth asked, putting aside the partial conversation that they had had in the hotel. "Surely we haven't changed that much?"

"Our situation has changed." John stated honestly. "And I just have a feeling that it is going to get worse before it gets better."

Elizabeth was shocked. "What happened to that cocky, fly-boy attitude that you used to have?"

"It disappeared." John stated sincerely. "I mean it's still there...but that cocky, fly-boy attitude has gotten a lot of people killed."

"I'm still here John." Elizabeth stated quietly, knowing that her words held more than she was saying. "I'm still here."

"I know." John said with a nod of his head. "Believe me Elizabeth I know..."

* * *

A/N- Hey gang! Thank you to sparklyshimmer2010, StormO, saphtiretwin369, jasminesmommy, Jenni, Charmed225 and whirlwind2005 for reviewing the last chapter. I hope that you guys liked this one and will review it too. :D 


	10. Part I: Still Human

A/N- I HATED 'This Mortal Coil' I totally hated it! I mean, it was an okay episode. Right until the end... and I am totally glad that I have been changing things. Er- and on that note this is the last update for a while, at least until 'Be All My Sins Remembered' is shown on TV in the new year.

Still Human

Things were really strange. They had discovered that there was another team out there. A duplicate organic copy of all of them created by Niam's faction of the Asurans- and they needed to meet with the real thing. But they were not prepared with what they encountered.

"They told me that you were dead." The duplicate Elizabeth stated as soon as her real self stepped through the gate. "That I was the only one."

"Well," The real Elizabeth stated with a bitter grin. "At the moment, you're more real than I am. You just have the little buggers within you to heal. I have them as part of me."

"Half replicator." Duplicate Elizabeth whispered in shock. "How horrible that must be for you."

The real Elizabeth grimaced. "You have no idea."

---SPARKY----

"It's the strangest thing." Elizabeth stated as she and John took a walk through the forest. "Looking at another copy of you, and me and the team..."

"I know." John agreed holding his gun to his chest. "I don't know what to make of all of it."

"I think I do." Elizabeth stated with a sigh, knowing that what she was about to suggest could and probably would cripple John.

"I know that look," John said worriedly. "What are you thinking?"

"I'm thinking that no matter what happens, the other Elizabeth should go back with you."

"What!?" John asked, not believing what he was hearing. "Why in the world-"

"Think about it John," Elizabeth stated with a sigh. "She's me in every way only she's fully human. She has nanites yes but they are there to repair her, they don't make up half of her. Not like me."

John just stopped in his tracks causing Elizabeth to pause as well. "Elizabeth," he began his voice full of pain and anger and another emotion that Elizabeth wasn't willing to name for the moment. "I-"

"John it's the best for both of us." She stated, echoing his words to her from long ago. "I can go and she can stay. It will be exactly the same."

"Except that she won't have the past few months of memories with us." John pointed out, thinking specifically of their conversation in the hotel room on Earth. "That's not the same."

"John it could be safer for all of us in the long run." Elizabeth stated with a determined glare. "I am going to do this."

"I won't let you." John stated determinedly. "I can't lose you."

"You won't be losing me." Elizabeth insisted.

"But I will." John argued. "She may look like you; talk like you but she will never, ever be you."

"John,"

"Elizabeth you made me walk away from you once," he stated firmly thinking of when he had orderd him to go on the replicator homeworld. "I am not prepared to do that again."

"John..."

"Elizabeth." He interrupted, fully prepared to say what he had wanted to say for a long time. "I-"

"Shh..." She interrupted, raising her hand to silence him.. "Do you hear something?"

---SPARKY----

It was over. Both visions had come true. The other Atlantis-class city had been destroyed and when they had gone back to check on the planet the jumper was crashed with no sign of its crew. They figured that the replicators wouldn't be so stupid to think that they had all died but at least they had gotten away.

"I knew that I would find you here." John stated as he came out onto the balcony. "You always come here."

"I know." Elizabeth, his Elizabeth- the Elizabeth that was still half-replicator stated with a sigh as she looked over her shoulder. "The sea is so calming. Even through I still haven't gotten used to two moons."

"I know what you mean." John stated as he joined her. "I'm so glad that you decided to stay."

Elizabeth sighed. "Honestly, I don't think that it was the right choice but-" she shook her head. "I guess after all this time fighting I was ready to stop. But I couldn't..."

"Held back were you?" John asked his voice in hushed tones.

"Yeah," Elizabeth agreed her voice equally as quiet. "By you."

"What?" John asked, not getting the answer he was looking for. "Me?"

"Yes." Elizabeth agreed with a sigh- something that she seemed to be doing a lot lately. "You're the only one who's been able to convince me that despite everything I'm still human."

"Of course you're still human Elizabeth." John stated insistently. "And we'll find a way to get those little buggers out of you."

"I don't know how we're going to do that," Elizabeth stated with a sigh. "...but I believe you."

"Good." John said. "We'd miss you to much."

"Oh you'd all get along just fine with out me." Elizabeth stated, rambling on to protect her feelings. "I mean I hardly do anything around here as it is and-"

"No." John interrupted, trying to get his point across. "I'd miss you."

That caught her off guard, and although she wanted to say something witty or nonchalant; she couldn't. She had waited to long and decided not to wait any longer. Slowly, she inched forward to John and pretty soon their mouths were mere inches apart, and then they weren't apart at all.

The kiss was tentative at first, but as it deepened it became full of passion and Elizabeth wrapped her arms around John's neck while he hugged her seemingly fragile body to his chest. When they finally broke they just looked at each other- shocked at what they had just done.

"I-" He was at a loss for words, but Elizabeth always the diplomat knew exactly what to say.

"I never knew that you felt the same way." She stated with a smile. "I've tried to tell you."

"I know." John stated not letting go of her waist. "But I thought...well to tell you the truth I didn't know what to think."

"At least you know now." Elizabeth sated with a smile. "But where do we go from here?"

"Well, I was thinking a dinner on the western pier. I hear from Rodney that the sunset from that vantage point are just amazing."

"You know I'd like that." Elizabeth stated giving John another chaste kiss on the cheek before leaving. "Swing by my quarters at seven tonight?"

"It's a date then."

And as John Sheppard watched Elizabeth walk away he knew that everything had changed for ever- and for the better.

* * *

A/N2) Thank you to saphire, samy, Strom, Serised, sparkly, Jenni, Charmed and Jasmine for reviewing the last chapter. I hope that you guys are enjoying this- especially this chapter since our dear sparky made some serious headway with their relationship. :D And I hope that you guys will review this chapter too. :D Till 'BAMSR' is aired beloved readers, till then. 


	11. Part I: Make A Choice

A/N- 'BAMSR' was...oh how do I say it? Damn brilliant? Yes, it was damn brilliant. Not only did they bring back- or rather confirm that least an incarnation of our dear Lizzie is alive, but the replicators (or at least most of them) seem to be dead. All in all I'd call that a win...but how to incorporate Elizabeth into this episode, when a) she was already in it and b) I love the whole Elizabeth in control of the replicators thing... So, my canonically correct plot with Elizabeth in it may descend into AU 'cause I've got a bloody brilliant plot idea...which maybe I should for- nah. Never mind. 'Nuff rambling from the author- here's the next long awaited instalment of 'What Would Elizabeth Do?'

P.S- Slight spoilers for 'Ark of Truth' if anyone cares

Making a Choice

The briefing had not gone well and as Rodney stormed out both humiliated and furious Elizabeth could barely keep her anger in check. Especially when Ellis started spewing nonsense again, "I don't understand how you guys put up with..."

"Colonel," Elizabeth interrupted not able to keep it to herself anymore. "May I remind you that Dr. Rodney McKay is one of the most brilliant minds in two galaxies and that he has not only saved Atlantis from certain doom far too many times to count, but that he has also saved my own life on more than one occasion."

"I don't see your point."

Elizabeth glared at him. "The point Colonel is that Rodney may be the only one able to save us in the end. So I suggest that you simmer down, shut up and let the man do what he wants and not bait him nor humiliate him in front of his colleagues again because he is way smarter then you are."

"Dr. Weir-" Ellis began his disgust for Elizabeth well evident on his face. He hadn't liked it when Elizabeth was allowed to remain on Atlantis, he had thought that she was a security risk and didn't want to have anything to do with her but still- he had no choice.

"Colonel," Sam interrupted an equally evil glare on her face. "If you _ever_ talk to someone under my command the same way that you talked to Rodney just now I will ensure that you will never be welcome back on this base ever again. Is that clear."

Taken aback by Sam's harsh words Ellis nodded. "Yes, it is."

"Good." Sam stated turning to look at John, Caldwell who had remained almost silent and Elizabeth. "We're done here, thank you."

They all filed out one by one with Elizabeth being last in line. "Hey Sam," Elizabeth stated as she was the last one in the room. "Can I say something?"

"What is it?" Sam asked with weary but open eyes.

Elizabeth smiled. "Thank you."

Sam nodded knowing full well what it was like to be in her position and Rodney's. "You're welcome."

-sparky-

Things were spiralling out of control. "You did what?" Elizabeth asked as she peered into Rodney's office. "Rodney, how could you?"

"Well uh- it was either this or nothing," he defended. "I know that-"

"No." She interrupted sternly. "I don't think that you do know. Colonel Carter is not going to like this and John..." she paused and chuckled with the irony. "...he is going to see this for what it is; a security risk."

"You know," Rodney began remarking with amazing clarity what he had been noticing for months. "You're becoming more like him."

"What?" Elizabeth asked fear clutching her heart as she wondered if Rodney had figured things out. "Like who?"

"Sheppard," Rodney remarked. "You've been seeing the military side of things since we rescued you and he well- he's become much more 'talk first and shoot second' which isn't like him..."

Elizabeth was caught off guard. "People change Rodney," she stated finally. "Look and me..." then with a smile she added; "...look at you."

That caught Rodney off guard and he had to agree with her. "Yes well uh-"

"Dr. Weir? McKay?" Carter's voice sounded stopping Rodney's sentence before he could really begin. "They're back."

-sparky-

"John?" Elizabeth asked catching up to John and Sam as they walked through the halls of Atlantis.

"Hey!" John stated his face lighting up, something that did not escape Carter's notice. She had heard through the rumour mill that she had disappeared into his quarters a couple weeks ago, just after the incident with the organic replicator clones and had not come out again till the next morning. Sam assumed that she should talk to them about it, but then she remembered that Elizabeth was just a member of the Atlantis expedition and therefore having any sort of intimate relationship with John was no different then Katie and Rodney getting together.

"I was just coming to see how it went." Elizabeth continued breaking off Sam's train of thought. "How many ships do we have?"

"Fourteen," John answered, his smile not diminishing as Elizabeth fell in step beside him. "Larrin said that she can get three or four more ships."

"Well that's great." Elizabeth exclaimed her heart lightening a bit- she had not liked the thought that her newly formed relationship with John would end just as it had begun on account of some stupid replicators. And yet, even as Elizabeth smiled in enthusiasm she could see that something was wrong. "John?" she asked, her concern evidence in her voice. "Are you okay?"

John was about to respond when Carter interrupted him her hand still on her radio. "John," Sam began, "Rodney wants to see us as soon as possible in my office."

"Just lemme have him for a couple minutes." Elizabeth stated, flashing Sam a smile that caused the new commander of Atlantis to nod, pushing down her own wave of jealousy as she heard Sam call the office her office. "So," she continued as Sam was out of earshot. "What's wrong?"

"I took Teyla off active duty."

This she had been expecting and thus wasn't surprised, but for John's sake she feigned innocence. "Why?"

"She's pregnant."

Elizabeth nodded as though she was shocked. "That would be a good reason." She smiled sympathetically and placed a comforting hand on his shoulder when suddenly he caught her eye and in that instant she knew that he knew.

"You knew!?" he whispered so as not to draw attention. "You knew and you didn't say anything to me?"

"It wasn't my secret to tell," Elizabeth explained her voice no more above a mere whisper. "What would you have me do?"

"I would have thought that my girlfriend would let me know when our mutual friend is putting herself at risk." John stated causing both himself and Elizabeth to stop for a moment at the word 'girlfriend' for they had never actually talked about their status, and John knew that now wasn't the time. "How long have you known?"

"Since the Athosians went missing," Elizabeth answered with a sigh while her mind tried to process why John had just skipped over the fact that he had called her his girlfriend. "She told me when I visited her that night in the infirmary. Listen I'm sorry but-"

John dismissed her apology with a wave of his hand. "Don't apologize, I know that you were in the right, and I was wrong to think that you should have told me," he flashed her one of his flyboy grins and then continued. "Come on, let's go see what McKay has done now."

Elizabeth groaned causing John to look at her. "You know?" he asked watching as Elizabeth didn't try to lie but merely nodded instead. "What do you know?"

"What he's done." Elizabeth answered taking his hand and leading him towards the control tower. "But I can't explain it- better leave that to Rodney."

-sparky-

"Does she know why she was created?" Elizabeth interjected looking at the image of the replicator on the screen. "I mean does she know what her purpose is?"

Rodney nodded. "Of course."

"Then she has a certain amount of self-awareness." Sam added.

"Yeah," Rodney agreed. "So?"

"So?" Sam asked cutting of Elizabeth before she even began. "Honestly I'm not sure how comfortable I am sending her to her death."

"Death?" Rodney asked himself in amazement. "It' can't die! It's not alive! It's a programme! I mean it's consciousness is just a bunch of ones and zeroes. I mean you can call it 'she' all you want but it's still just a thing. It's a prop- it's a really advanced radio-controlled weapon. I mean, you don't feel sorry for your bullets do you, your bombs?"

"Rodney?" Elizabeth asked sharply causing all eyes to fall on her. "She's alive, she's aware. That makes her more then a simple bomb or bullets. Those things have no intelligence, but that replicator there...why she's just like me."

"She is NOT just like you."

"Rodney," Elizabeth began again. "She is just like me. She has nanites keeping her alive, I have nanites keeping me alive. The only difference is that I am half organic- but even that isn't a difference. I have feelings and memories and we know first hand that the replicators have them too."

Rodney was becoming uncomfortable. "So what do you propose that we do?"

"I propose that we give her a choice." Elizabeth stated plainly hardly noticing that over the course of her rant that John had come to stand beside her. "I say that we let her know what it means to be human and then let her decide if she wants to take this mission on."

Sam nodded in agreement, "I agree with you Elizabeth but there's only one problem, what if she doesn't want to do it?"

Elizabeth looked from Rodney to Samantha and finally to John before turning her gaze back to the replicator on the screen. "Then I'll do it myself."

"_WHAT?!?_" Rodney and John nearly shrieked at the same time.

"No way," Rodney muttered.

"Damn straight no way," John agreed forcing Elizabeth to turn and look at him. "Why would you want to go on a suicide mission?"

Elizabeth smiled at him poignantly. "Why did you go on that suicide mission?" she asked watching a slight understanding come over John's face. "Because you had to," Elizabeth stated, saying what John was thinking. "And that's why I'll do it- because it has to be done...one of us needs to make a choice and if the replicator that Rodney's created doesn't want to then I will...the needs of the many out weigh the needs of the few."

"That's from Star Trek," John pointed out with a small smile.

"Doesn't mean that it's not true," Elizabeth said.

"Yeah well John's not Kirk and you are not Spock so don't give me that whole 'needs of the many' crap." Rodney stated angrily. "And besides it wouldn't work."

"Oh no?" Sam asked curiously. "Why not? Not that I'm saying that I approve Elizabeth but it doesn't hurt to have a plan b..." she smiled at the former leader of Atlantis and then turned her attention back to Rodney. "...so why won't it work? Elizabeth's nanites are the same as this replicators are aren't they."

"Strictly speaking..."

"Aren't they?"

Rodney sighed. "Of course they are and if I had to..."

"Well lets just hope that you don't have to." Elizabeth interrupted with a small smile. "Because believe me, I don't want to go anywhere." She turned to face John whose hands had dropped to her hands. "I have too much to live for."

-sparky-

Sam knew. How could she not know? She had seen the way that Elizabeth had looked at John and how she had reacted whenever he was in serious peril, but what she hadn't been expecting was that the second in command and the former leader would actually get together. And yet, the way that John and Elizabeth were arguing on the balcony made it all the more obvious.

Sam knew that with Fran agreeing to complete her mission that they wouldn't have to sacrifice Elizabeth- not that anyone was actually considering letting Elizabeth sneak into the replicator city and be the ticking time bomb- and yet Sam was still surprised that Elizabeth was arguing to go.

And as Sam watched John and Elizabeth argue she could see how their relationship had grown in the last couple weeks. To persuade her, John took Elizabeth's hands into his own, and put his hands lovingly on her face, Elizabeth in turn did the same and after a while Sam felt as through she had to walk away.

Making her way back to the office Sam wondered how they found the strength to be together. 'This galaxy is so full of peril,' she thought as she made her way through the final battle plans. 'anyone of them could die at any given moment...' Sam sighed and placed her pen down. '...but of course, being together makes all this time the more precious and more special, and that makes it all worthwhile. They are making a choice and sticking by it...'

There was a bitterness in her head that Sam didn't like having. For eight years she had pushed down the feelings for her own commanding officer and then when they were finally not in the same chain of command he would have nothing of it. And so Sam was left pining away for something that would never be... 'And then along came Cameron,' she smiled as she thought of the sparky young colonel who had reformed SG1 and pulled her along for the ride of her life.

'How I miss him...' and indeed Sam had grown incredibly close to Cameron and after they had saved their own galaxy from the Ori she had gathered enough courage to give him a slight kiss on the cheek. That kiss she had hoped would turn into something more, but giving the next crisis there hadn't been the time- and then of course, Atlantis had called and Sam like the willing solider she was followed.

"Colonel Carter?" Elizabeth asked standing in the doorway to her former office. "Sam?" she asked again causing the new leader of Atlantis to be broken out of her thoughts. "I uh- just thought you should know that Colonel Sheppard has managed to talk me out of joining the team on the mission."

Sam smiled. "Good. You'll be in charge of the city until we get back."

"I'd like nothing better."

-sparky-

"Welcome back," Elizabeth stated with a broad smile as John was beamed down onto the inner balcony of Atlantis over looking the gate. "It's good to have you home."

"It's good to be home." John stated with a cheeky smile turning from Elizabeth to Rodney who was busy on a computer. "How goes our good friends the Wraith?"

Rodney could do nothing but sigh. "They never showed up at the rendezvous point and I doubt that they could have gotten caught in the explosion. The most rational answer is that they knew that there was nothing left for us to talk about so they just went along their merry way and we're back to being enemies."

Elizabeth sighed. "Back to being enemies with the wraith, the replicators don't exist anymore... can we count this as a win?"

"Oh yes," John agreed. "We can defiantly take this as a win."

"Oh yes, all is right in the world," Rodney stated with a roll of his eyes. "-and speaking in being right with the world I've just deleted the replicator home world from our database which was actually a lot harder then one would have thought."

"M7R-227 you were a complete pain in the ass," Elizabeth stated with a smile as the light on the screen designating the planet disappeared into oblivion. "It is so good to see you go."

John sighed. "If only it had been this easy."

"Mmm," Rodney agreed closing his laptop. "Area 51's working on it."

Elizabeth smiled. "That's good to know," she turned to face John. "Do you wanna get a late dinner?"

"Absolutely."

"Can I come?" Rodney asked watching as Elizabeth and John turned to leave together. "To uh- eat dinner with you guys?"

"Sorry Rodney," John apologized looking over his shoulder. "But this is a dinner for two."

"_Stupid lovebirds_..." Rodney muttered under his breath as John and Elizabeth left the control room hand in hand. "Stupid, _stupid_ lovebirds."


	12. Part I: Comfort

A/N- So after the awesomeness of 'TMC' and 'BAMSR' I'm sad to say but 'Spoils of War' was kinda ho-hum; so sad. And yes sparklyshimmer2010, that was a Camantha reference in there and I am a proud shipper of Cam/Sam. And the part about the kiss in the last chapter is actual canon stuff- that's why I said slight spoilers for 'AOT' the movie. And now, enough rambling...here's the chapter.

Comfort

The latest crisis had been averted- barely. John and his team had come across a rogue wraith cloning facility that would have given them a huge advantage. But luckily they had managed to stop them- thanks to Teyla. And yet- there had been unforeseen problems.

"I really should go and talk to her," John whispered to Elizabeth as they watched Teyla watching the stars further down the balcony. "I mean, I am her commanding officer."

"I know," Elizabeth agreed with a sigh as she leaned into John's arms. "But I'm her friend and a girl to boot, it should be me." John had no arguments with that and therefore Elizabeth crossed the short distance and stood beside her dear friend.

"Did you talk to Keller?" Elizabeth asked softly as she leaned on the railing.

Teyla nodded. "I've just come from the infirmary. Everything is fine," she paused looking uncertain. "-at least physically."

Elizabeth was both confused and worried at that. "What does that mean?" she asked, and when Teyla merely sighed Elizabeth began to worry. "Teyla?"

"I exposed my unborn child to the mind of a killer," she whispered hatred and self-loathing and despair evident in her voice. "-even before he has opened his eyes on the world."

That caught Elizabeth off guard. "He?"

Teyla smiled. "Yes, it is a boy."

"Really?" Elizabeth asked. "I thought that you didn't want Keller to tell you the sex of the baby. That you wanted to keep it a surprise."

Teyla smiled softly. "She didn't." Seeing the confusion on Elizabeth's face she continued. "When I was fighting the wraith queen, my son was there with me- fighting right along side me. I drew on his strength to protect the two of us and he did the same...that is how I know."

Elizabeth was floored. "I had no idea the bond between mother and child could be that intense, that intimate."

Teyla nodded. "It is rare among my people, some children are born with the knowledge of those early communications with their mothers- but it fades with time in most cases. I myself can remember nothing but Charon could remember almost everything, right up until the day she died."

"It must be a comfort." Elizabeth pointed out. "Having him inside you."

Teyla nodded again. "Yes it is, and yet..." she sighed and turned to face her lond time friend. "...I have begun to question my involvement in the mission. There was a time when I would have laid down my life for John, Ronan and Rodney without hesitation if I had been in that situation alone..."

"But you're not alone anymore." Elizabeth finished understanding perfectly. "You have other things to think about."

"Yes," Teyla agreed with a heavy sigh. "My child must come first."

"That's completely understandable."

Teyla sighed again and Elizabeth could see tears glistening in her eyes. "Elizabeth, you have no idea how close she came to extinguishing her life. If John had hesitated even for a moment then my son would have..."

"Your son is alive." John interrupted coming over to stand beside Elizabeth unable to not talk to Teyla any longer. She was his friend and team mate and he had to ensure that she was alright. "Your son is alive and so are you. If you want to stay on Atlantis on further missions then you'll get no complaint from me. We'll keep an eye and ear out for your people. We'll find them..." he paused and smiled at Teyla. "...you can trust us."

Sniffling, Teyla nodded her head and crossed the short distance and gave him a thank-you hug. John awkwardly returned it but when Teyla pulled away and moved to Elizabeth he watched as the two most important women in his life clung to each other. Teyla needed the support that Elizabeth could give and Elizabeth was only too glad to give it.

And as John watched them he couldn't help feel sorry for Teyla and he couldn't help but wonder what would happen if he and Elizabeth ever decided to have a child. They had never talked about it, nor even attempted to broach the subject but John couldn't help but wonder. The Pegasus Galaxy was such a dangerous place and nothing was certain... but what was certain, John decided finally was that so long as they were all together then that's all that they could ask for.


	13. Part I: Ready or Not?

A/N- So 'Quarantine' was one of the better episodes as of late, although the ending kinda sucked yet despite that- doth mine eyes see a brand new ship? Me thinks that mine eyes doth not lie. :D So all in all- only a couple things to fix and I hope that you guys will like those little fixes.

Ready or Not?

It had been months since a problem had occurred. Teyla was in the fifth month of her pregnancy and going strong and while John and Elizabeth were going strong, Rodney and Katie seemed to be going stronger. The occasionally nervous, apocalyptic and naysayer scientist had just told his best friend what he was planning to do- and John had only five words to tell him.

"Well, go get the girl!"

Stunned for a moment Rodney pointed towards the door made an incoherent sound and then put the box into his pocket again before heading towards the exit only to bump into Elizabeth.

"Hello Rodney."

"No-" Rodney snipped. "Can't talk."

"Rodney!?" Elizabeth chastised causing the scientist to pause in his tracks. "What's going on?"

"I uh-" Rodney paused and turned to face one of his other best friends. "I'm uh going to propose marriage- to uh- Katie...?"

Elizabeth's eyes widened. "Congratulations Rodney," she stated with a smile. "I'm sure she'll say yes." Slightly more nervous now Rodney nodded and then disappeared down the corridor leaving Elizabeth alone with John. "Hello sweetie," she said with a wider smile as she came into Rodney's lab. "Can I talk to you for a moment?"

Smiling, John nodded. "Of course, we always talk."

"I know," Elizabeth agreed her face getting a little more serious. "But this isn't about us-"

"No?"

Elizabeth shook her head. "No, it's about Teyla."

John groaned. "Oh don't tell me that she asked you to talk to me about putting her back on active duty?"

"No," Elizabeth said a little shocked that John thought that. "I mean, not really. She uh wanted to know what you would do once the baby was born."

"Well uh, she takes it easy for the next couple months then has the bouncing baby boy, takes another couple of months and then is welcome back." John answered with a shrug of his shoulders. "No questions asked."

"Well she has a couple of questions."

Now, John was intrigued. "Oh yeah?" he asked. "Like what?"

"_Elizabeth," Teyla stated coming up to her former leader. "May I talk to you for a moment?"_

_Elizabeth nodded. "Of course Teyla, what's up?"_

"_I was- the thing is..."_

"_Teyla?" _

"_I am worried for the fate of my child should anything happen to me when I rejoin John's team after he is born." Teyla sighed and shook her head. "I know not what to do, Elizabeth- could you speak to John for me? Perhaps he will have some insight, or a decision that I can live with."_

"You did tell her that should anything happen to her that her son would have a family here," John paused and looked at her girlfriend. "Right?"

Elizabeth nodded. "Of course, she's still worried though and I-"

Elizabeth's sentence was cut off when suddenly an alarm sounded and the large blast door leading out of Rodney's lab slammed shut. Instantly Elizabeth and John were on their feet and at the back door. Elizabeth ran her hand repeatedly over the wall panel but it beeped negatively each time. She shook her head and stepped aside so that both she and John could try to open it manually but that didn't work either.

"We're locked in,"

John nodded in affirmation and then activated his radio headset. "Rodney come in..." Meanwhile Elizabeth kept trying to get the wall panel to activate with no such success. John kept trying to raise Rodney over the radio before just giving up. "Communications are down..." he sighed and walked over to the blast door that lowered down while Elizabeth went to check the computers. "What I wouldn't give for Ronan's gun right now."

"John, come here a sec-" Elizabeth stated as she pointed towards the computer screen. "It looks like there's been another outbreak."

"What?" John asked, horrification slipping into his voice. He instantly walked over to her and called up the information from the laptop to the larger screen. To their dismay it showed a schematic of the city all outlined in red. He then pressed a couple of buttons and more screens popped up showing more information the last screen to do so reading **–CATEGORY FIVE QUARINTINE INITIATED-** which caused the both of them to groan.

"Category five?" Elizabeth asked putting her hands in her hands.

"I'm guessing that it's a lot worse than categories one through four..." he sighed and sat down beside her. "We could be here a while," then a thought crossed his mind. "What was the outbreak a few months ago?"

"Category two," Elizabeth answered. "But the city didn't go into lockdown then."

"Alright," John said. "What about the one our first year here."

"I don't think that Rodney had the rating system back then,"

"Well," John argued, irritation coming into his voice. "What would have classified that as?"

"Considering that it locked down the entire city once it was defected-" Elizabeth began irritation in her voice as well. "-I'd say a category five. But that's just me."

Knowing that she was upset, John placed a comforting arm around her and leaned into her ear. "I'm sorry," he whispered. "I just hate not knowing what's going on."

"I know," Elizabeth replied with a smile. "I don't like knowing what's going on either..." she sighed and then straightened up. "Maybe we can find something on the computer."

And so, both John and Elizabeth went to work and within half-an-hour they came across some major information. "Well, looks like there are life signs all over the city," Elizabeth stated. "Looks like everyone is trapped like us, which is odd meaning that the outbreak is spreading faster then we've seen previously"

"Looks like ventilation is down too," John stated as he typed away on the second laptop. "That means that the people down in the more isolated sections are running out of air."

"Oh god," Elizabeth moaned the gravity of the situation weighing even more heavily on her mind. "I hope that no one was trapped in the transporter or the-"

"Rodney," John moaned as he noticed Rodney's radio earpiece lying on the table beside the second laptop. "He's in the Botany Lab."

"I know," Elizabeth agreed. "I knew that but I don't see how-"

"Have you ever been there Elizabeth?" John asked, tilting his head to the side. "It has to computers and no radios and-"

"And if Rodney's locked in there-"

"Which we can assume that he is..."

Elizabeth sighed. "God he's going to be freaking out about this. He won't know what's going on or how much of the city is in lockdown or..." she sighed and went back to her laptop muttering. "We better figure this out soon."

A couple hours later after sifting though a lot of data Elizabeth stumbled upon something; "John, it looks like there was a disturbance in the planets ionosphere a few hours ago- moments after that is when the systems became unstable."

"New planet, new problems..." John muttered.

"This means that there might not even be an outbreak," Elizabeth pointed out. "And even thought the cities in lockdown it must be a malfunction, meaning that we'll be able to fix it-"

"You mean that Rodney will be able to fix it but if he can't a hold of a computer then he's not going to be able to shut it down."

Elizabeth groaned. "Maybe Zelenka or Colonel Carter will be able to-"

"If either of them had access to a computer then they would have done it already." John pointed out. "That means that they probably can't get a hold of one either."

"Can anyone else do it?"

John shook his head. "They probably could but they'd need to know Rodney's password," John paused and he noticed that Elizabeth sighed and inside, John felt a little elation knowing that he was going to be able and be the hero. "Fortunately I know it."

"Rodney told you his password?" Elizabeth asked her eyes widening as she looked at her boyfriend. "Why would he tell you it?"

"I'm sure that he didn't think that I'd remember it." John stated with a chuckle.

"And why is that?" Elizabeth asked knowing that mischievous laugh.

"We were kinda drunk at the time."

"John," Elizabeth chastised causing John to laugh even harder.

"Just be thankful that I got it out of him," he stated with a smile as he began to type. "One, six, four, three, one, eight, seven, nine, one, nine, six, eight, four, two..." They both waited with baited breath for the computer to beep. Once it had John sighed in relief. "See, it doesn't take a genius to do it."

"But a genius managed it." Elizabeth pointed out with a smile. "How'd you remember the numbers?"

"It was easy," John answered with a smile. "1643 was the year Newton was born; 1879 was Einstein and 1968 was-"

"The year that Rodney was born," Elizabeth chuckled and shook her head in amusement. "The ego that that man has..." she smiled but then remembered the final two numbers, "The final two numbers were four and two right?"

"Right."

"As in forty-two?" Elizabeth asked again eliciting the same response from John who was continuing to type.

"Right."

"As in the ultimate answer to the greatest question of life, the universe and everything?"

"You know the 'Hitchhikers guide'?" John asked with a bewildered look before the computer beeped signalling that they were in. But as soon as John looked at the screen he wished that he was still locked out. "Crap."

"What?" Elizabeth asked her panic returning. "What is it now?"

"Part of the lockdown programme that Rodney created included a warning beacon for approaching ships,"

"To let them know about the outbreak," Elizabeth finished knowing full well what Rodney had created. "Oh god- it's broadcasting now?"

"Yeppers." John confirmed. "And there's no way to turn it off 'cept from the control room and-"

"And if the people in the control room had noticed it they would have turned it off already or they don't have the password," Elizabeth finished with a sigh. "If we don't turn it off Atlantis could be discovered by the Wraith."

"If it hasn't already happened," John muttered his sense of doom and gloom growing. "We need a plan."

"And what do you propose that we do?" Elizabeth asked. "The blast door is closed, the other exit is closed leaving the only thing the window and-"

John's face lit up and Elizabeth knew what he was thinking. "No." she stated firmly. "No. You can't. I won't let you."

Not listening John walked over to the window overlooking the city and then picked up the stool which stood underneath it and then took a couple steps back. "Okay, stand back Elizabeth."

"John-" Elizabeth protested but it was too late, the window was broken and John was already halfway out the window. "You are not going to do what I think you're going to do."

"The control room is only four floors above us," John pointed out with a determined grin. "All I have to do is climb up and then I'm in."

"Climb the tower..." Elizabeth stated. "Is that even possible?"

"I'm going to find out." John stated as he stepped onto the window sill and the narrow ledge outside. "Besides Batman did it all the time."

"But you're not Batman." Elizabeth pointed out as she poked her head out the window to look up at John.

"What about Superman?" he asked with a cheeky grin.

Elizabeth shook her head. "I'm sorry, you're not," she sighed and looked up and was barely able to see vents and shafts and what looked like plenty of handholds. "You think you can do this?"

"Piece of cake," John answered his voice being carried away by the wind. "Don't worry, I'll be fine. I'll just climb up turn off the beacon and-hey!" John's sentence was cut off by the jostling of Elizabeth who climbed out of the narrow window to join him on the ledge. "What are you doing?"

"Climbing up with you,"

"Elizabeth-"

"Listen," she began her hair blowing every which way in the wind. "I know that I can't stop you from doing this, but hell will freeze over before I sit in Rodney's lab and let you risk your life..."

With a simple nod John agreed and together they began to climb. Every so often one of them would lose their foothold or handhold and the other would scream and nearly panic but it was as though they both had their guardian angels with them that day because they made it to their balcony in one piece. Upon seeing that it too was sealed they reached for the nearest planted tree and threw it through- much to the surprise of those who were already within the room.

"Colonel?" Chucj asked as John stepped through the gap followed by Elizabeth. "How did the two of you get out there?"

"Long story," John muttered as he ran over to the console.

"We climbed," Elizabeth answered noticing the look of confusion on Lorne's face. "We've got to turn off the beacon, it's broadcasting our location and-"

"And we tried," Chuck replied coming over as John was imputing Rodney's password. "But none of us had the right code and-"

"What's going on up here?" Lorne asked as he ran up the stairs followed by the other scientists. Upon noticing the Colonel he was most surprised. "Where the hell did you come from sir?"

"The beacon's deactivated," John stated with a smile as a wave of relief washed over him- but then another alarm sounded and all the computer screens went dark. "Tell me that's not the self-destruct."

"It is," Chuck answered at one of the dead laptops. "And all the computers are dead."

"Why would you arm the self destruct?" Elizabeth asked her eyes wide.

"I didn't." John answered just as the alarm shut off.

"Thank god," Lorne muttered with relief.

"You shut it down?" John asked turning to Chuck.

"No sir," Chuck replied. "Just the alarm, and the city actually armed the self destruct by itself Doctor Weir."

"Why would it do that?" Elizabeth asked just as realization dawned. "Wait- don't tell me...the city saw that the quarantine had been breached and blowing up the city was the only other course of action."

Chuck nodded. "That's what I would assume ma'am, especially from what I could gather from the screens before they fell dark."

Elizabeth groaned and looked at the broken door. "It was us, the city thinks that the disease is spreading."

"But there isn't a disease," Lorne pointed out.

"I know that," John agreed. "And you know that- but the city doesn't know that..." he sighed and crossed his arms. "What we have to do is turn it off manually which is-"

"In the main power room," Chuck answered. "Six levels down."

"So I climb back down,"

"No." Elizabeth argued standing beside John. "We'll come back down, but what do we do when we get there, the power distribution is in the centre of the tower."

John nodded and then turned to Lorne. "Got any C4?"

"Some," Lorne said as he reached into his vest pocket and took out one small block. "But this is it."

John grimaced and then looked to Chuck and Elizabeth. "Okay, Lorne and Chuck you're with Elizabeth and me."

It took nearly half as much time to climb down as it took to climb up and pretty soon John was putting the last of the C4 onto a set of interior doors. Once he was beside Lorne, Chuck and Elizabeth he took out the detonator. "Fire in the hole," he stated as he blew the C4 causing a loud explosion. They walked through the doors and instantly heard muffled shouting.

"Oh god," Elizabeth muttered running over to the nearest transporter. "Someone's in here."

"Grab a side," John ordered as he took Elizabeth's side allowing Chuck and Lorne to take the other. Together they managed to get a hold of the main handholds and pulled the door open allowing both Radek and Sam to stumble out. "Colonel are you alright?"

"Zelenka," Elizabeth asked looking to the scientist. "Are you okay?"

"Yes," Sam nodded noticing that John was about to speak. "We know that there's no outbreak, it's a malfunction. Did Rodney manage to override that and the self destruct?"

"No," Elizabeth answered with a shake of her head. "The city is still in lockdown, the alarm has just been turned off and we haven't heard from Rodney. He was heading to the Botany Lab to propose to Katie."

The look of stunned faces made Elizabeth wish that she had kept her big mouth shut but it was too late, and Sam was the first to recover. "I've got to get to a computer-"

"You can't." Chuck answered. "They're all down."

"We were trying to get to the main Power Room so we can physically cut the power to the self destruct." Lorne pointed out. "But all the doors are sealed shut. We just used the last of our C4 getting here."

"Does that mean we're still stuck here?" Zelenka asked his eyes widening in horror.

"Looks like," John stated.

"How much time is left on the self destruct John?" Sam asked.

"We don't know," Chuck answered. "The computer shut down before we could see what the time was."

Sam sighed. "So it could happen at anytime-"

"Well this isn't good," Zelenka muttered. "What are we going to do now?"

"What _can_ we do?" Lorne asked. "There is no way to get out of this hallway."

"Does this vent go to the Power Room?" John asked pointing to the vent high on the wall.

"Yes, yes." Zelenka answered. "I believe it leads to the tower's main ventilation tube."

"Well, that system's shut down." Sam pointed out dejectedly. "Those vents will be closed off meaning that there's nothing we can do."

"But we can." Chuck answered. "Or at least someone can. The vents are open, or at least most of them are. We managed to get most of the tower back on before the computers went down."

While they had been talking, both John and Elizabeth had climbed on a chair, pried the vent cover off and John looked inside. He held out a hand to Lorne who was watching his military commander and handed him a flashlight. "Alright," John answered as he looked within the small shaft. "It's gonna be a tight squeeze, though – there's no way I can move in here."

"Lemme look," Elizabeth stated holding out her hand for the light.

"I'll do it." Sam offered.

"No I'll do it," Zelenka stated.

"Neither of you will do it." Elizabeth stated looking over her shoulder. "Zelenka, there's no way that you could manoeuvre in there. I'll do it."

"You sure?" John asked looking worriedly at Elizabeth.

"Yeah," she stated with a smile. "Should be a snap."

"Alright then," John agreed. "Just be careful." And then, together with Lorne he helped her with flashlight in hand, into the vent. After which they could do nothing but play the waiting game.

---sparky---

Within the ventilation tube Elizabeth felt as though all of Atlantis was closing in around her. "How could you offer to do this?" she asked herself out loud. "You don't know where you're going...not really, just the general direction at least-" she stopped her ranting to back up and turn a corner. "I'm going to die in here- it stinks..." she shook her head slightly and changed her mind. "No, I'm going to get lost in here and then Atlantis will blow up and we'll all die..." Elizabeth paused again as she came to a junction where her only options were to go straight, left, right or up. "Crap, guess down I go..."

---sparky---

"Come on Elizabeth..." John muttered as he shifted his weight uneasily.

"She'll make it." Sam comforted.

"I know she will," John agreed the worry evident on his face. "It's just that-"

"I know," Sam said causing a sharp look from John. "I know and I'm okay with it and if we get out of this you should really think of following Rodney's example. You'll never meet a better match for you then her."

Not quite knowing what Sam was saying, yet at the same time knowing exactly what she was saying, John was totally stunned and could only go back to his original statement. "Come one Elizabeth..."

---sparky---

Elizabeth fell headfirst through the vent and onto a floor. Dazed and groaning she stumbled to her feet. She could tell that her wrist was broken- yet she could already feel the nanites repairing it- and through the pain, Elizabeth gritted her teeth and walked to the power levers on the wall and pulled them all down causing the lights to go off before turning them back on and letting the lights light back up.

---sparky---

"You crawled the entire way there in those tiny vents?" Teyla asked with a smile as she, John and Ronan sat around a table that night in the mess hall. "I can't believe it."

"I can't believe that she fit in there."

"It was a tight squeeze," Elizabeth stated with a smile. "I could hardly move but the important thing is that I managed to turn the power off in time. Thank god Zelenka told me what to do."

They all shared a laugh and then Ronan turned to the group. "Did you guys here, McKay thought that it was a real outbreak and started getting sick; rumour has it that he thought he was uh-" Ronan paused noticing that Jennifer Keller was approaching their table. He dropped his feet from the spare chair instantly and sat up. "Hey..." he began. "Uh..."

Jennifer merely smiled. "Mind if I join you guys?"

"Sure," John agreed. "Go ahead."

Glancing at Ronan specifically Jennifer put her tray down first and then sat down herself. Ronan looked at her awkwardly then frowned at both John, Teyla and Elizabeth who were looking at him curiously knowing that something was going on. "What?" he asked causing the three of them to simply shrug.

"Hey guys," Sam began as she walked over the table causing the awkward tension to be broken. "It's been several hours now and there is no indication that anyone out there's picked up our alert beacon. I think we're in the clear."

"We should keep an eye out," Elizabeth suggested. "Just in case."

"Chuck is already on it," Sam agreed with a smile. "Thanks again Elizabeth, everyone on this base owes you their life."

"Oh I don't know about that..." Elizabeth stated with a modest shrug.

---sparky---

Much later that night, during the girls weekly card game- Elizabeth, Teyla, Katie Brown and Jennifer were all swapping stories of what happened when they had been quarantined.

"So Ronan nearly kissed you?" Katie asked here eyes wide as Jennifer turned red. "Why didn't he?"

"The lights went off," the young doctor answered with a shrug. "And then they came back on again, and the doors opened... it seemed kinda silly after that."

"But do you care for him?" Teyla asked an inquisitive look on her face.

Jennifer shrugged again trying to appear non-interested but her face betrayed her feelings. "I don't know. Ronan is such a mystery to me- I mean he might be in my infirmary three or four times a week with sparring accidents but-"

"Oh 'sparring' accidents." Elizabeth interrupted with a smile. "Ronan is a good sparring person, maybe he's getting hurt to just see you."

"Oh I don't know about that," Jen protested.

"I am in agreement with Elizabeth," Teyla agreed. "I have sparred with Ronan on many occasions and have only been able to beat him when something drastic was on his mind."

"So do you think he likes me?" Jen asked a childish glee bubbling up.

"Listen to me," Elizabeth stated sincerely. "A man does not try to kiss you without having SOME feelings for you. My guess is that he's got just as much a crush on you as you do on him..." then her brain kicked into gear and she turned to Katie. "Oh Katie- what about you? I know that Rodney was planning to- uh..."

"He was planning to propose to me today- or rather yesterday by this point," the red head agreed earning gasps from both Teyla and Jennifer who hadn't known. "But once everything was back to normal he came back to my lab to tell me that he wasn't ready, that he was rushing things."

"Do you think that he's rushing things?" Jen asked glad that the attention was off her.

"No," Katie stated. "That's the thing. He thinks that the way he is right now, well he thinks that he'll make me miserable. But he can't. I think that he's just so...loveable."

"Not quite the word that I would use," Elizabeth said. "But then again he did jump in front of a gun for me once,"

"And he has proven himself against both the Wraith and the Replicators on many occasions." Teyla agreed. "He is a good man and you would be lucky to have him by your side."

"I know that," Katie stated. "But the problem is that Rodney doesn't know that."

"Then you should make him know that Katie," Elizabeth suggested. "Make him see how you feel. If you think that marriage is the right thing for the two of you then go for it. Sometimes it takes the girl to push the guy."

"Speaking of the girl pushing the guy I overheard that Colonel Carter told John to follow Rodney's example," Jen said with a smirk on her face.

"Follow Rodney's example?" Elizabeth asked a funny feeling growing in the pit of her stomach. "What did she mean by that?"

But Jennifer didn't tell her, and Elizabeth didn't need her too. She knew that Sam had suggested that John should propose to her. 'It has been a couple of months after all,' she thought to herself and the four girls continued to play Euchre. 'And we have had strong feelings for each other for years...hell we're sleeping together and I love him-' That thought stopped Elizabeth's mind in its tracks. 'I love him,' she admitted to herself. 'And yet I've never told him...'

Then and there she vowed to herself that she would tell him when the time was right-after all, she was ready to make such a big step again.

A/N2- Wow. This was a good episode to convert. I can't believe how much I wrote! I hope you guys like this chapter as much as I do:D Please review! (Hey I made a rhyme!)


	14. Part I: Yours to Keep

A/N- So at the time of writing this chapter I haven't actually seen 'Harmony' but I've read the transcript and have realised that the only place to put our beloved Elizabeth in would be after...when John is recounting the entire adventure.

* * *

Yours to Keep

"So tell me the truth," Elizabeth began as she and John shared their customary evening walk along the balconies of Atlantis. "What really happened on M1A-272? The way Rodney's telling it he was the grand hero," she paused and noticed the scowl on her boyfriends face. "I take it that he's lying?"

"Oh yeah," John answered with a sigh. "See it all began at the celebration when the two older sisters Mardola and Flora asked us to 'guide' their sister. Of course Rodney called dibs on her and-"

"Wait," Elizabeth interrupted. "Rodney called dibs on the third princess? Isn't she like thirteen?"

John nodded. "Yeah but we didn't know that at the time-"

"But John, what about Katie?" Elizabeth asked. "I mean I know that he said that he wasn't ready for marriage but, I thought that they were still going strong."

"Yeah," John agreed with a shrug as he thought back to that moment. "That's what I thought..."

---sparky---

"_You are most generous," Flora stated with a loving smile. "Excuse us for one moment. I'll get her." She then left the room followed by Mardola and Rodney turned to John._

"_Dibs." He stated simply. _

"_What?!?" John asked, not sure he had heard him right. _

"_I'm calling dibs on the third sister."_

"_You can't call dibs," John stated. "What about Katie?"_

_That caused Rodney's demeanour to fall. "Right well uh- things aren't going so well between us right now."_

"_You're the one who revoked the marriage proposal." John pointed out. "She didn't turn her down."_

"_True." Rodney agreed. "That's true, but I uh-"_

"_Spit it out McKay."_

"_She came to me yesterday and said that she thought that I was selling myself short and that she thinks that I am ready to get married..."_

"_...and?"_

"_And I said that I needed time to think about it."_

"_Time to think about it?" John asked his temper exploding. "You've thought about it, you almost proposed to her. If that damn malfunction didn't happen then you would have been engaged by now."_

"_I know," Rodney agreed. "I know."_

---sparky---

"But you know Rodney;" John continued, thinking of the conversation that he and Rodney had had. "-he likes the admiration of the women we meet off world."

"And you don't?" Elizabeth asked with a coy smile, knowing full well about John's 'Kirk' association.

John shook his head. "I have you now," he answered with a small smile as he took her hand. "I mean even the marriage proposal from that little brat couldn't sway me."

"She- what?"

For once, Elizabeth was speechless and John had to laugh. And as he thought back to that particular moment in the woods, he could help but smile as he explained the conversation.

---sparky---

"_You know much about leadership John,"_

_John nodded. "Hard-learned lessons along the way."_

"_And I know much about my people."_

"_I hope so," _

_Harmony regarded John thoughtfully. "I think we would make a good team."_

"_Hmm?" John asked, not understanding and a part of him not wanting to know._

"_As Queen, I will one day need a King."_

_With that John looked away, his eyes wide. He wasn't liking how the conversation and he knew that he had to handle it carefully because Atlantis couldn't afford to lose the trade and ally. "Um listening Harmony-"_

"_There's no need to answer now." Harmony interrupted. "I know such an offer must be overwhelming. You shouldn't make your decision rashly."_

"_Well I am pretty sure I know which way I'm leaning." John answered. "You're a great little lady it's just that I'm involved with someone else."_

"_Who is she?" Harmony demanded to know her face growing dark. "I shall have her imprisoned for life."_

"_Oh I don't think so," John stated shaking his head. "She's a wonderful woman. Not only closer to my age but well..."_

"_You love her." Harmony finished with a knowing nod. "Love is very important. My mother was loved by my father, and I- even though I am Queen- can not begrudge you love."_

---sparky---

"Was she right John?" Elizabeth asked as they stopped at their customary place on the balcony outside of the control room. "Do you love me?"

"Elizabeth," John began his voice low. "You know how I feel about you."

"I think I know," Elizabeth stated as she placed her forehead against John's. "But being in my line of work you can only trust so much on what you know. You have to say what you know and have what you know said to you." She leaned her head onto John's shoulder. "I've been meaning to tell you this for a while John but I..." she paused and thought back to Simon briefly and all the hurt he caused her and decided that John was defiantly worthy the risk. "...I care for you a lot."

"I care for you a lot too," John answered as he cupped her chin and made her look up at him. "In fact-"

"I love you." Elizabeth blurted out, her voice barely above a whisper. "I love you," she repeated her voice a little louder. "I love you."

John was momentarily stunned and Elizabeth wondered if she had been wrong about how he felt but then his face broke into a smile and he kissed her passionately. And when he pulled away, he looked her square in the eyes.

"I love you too Elizabeth," he stated honestly and sincerely. "More than I've ever loved anyone my entire life. You- you complete me in a way my first wife never did and you've changed me for the better. I'm not so military driven, I think things through and I see the bigger picture and I want you in my picture for a very long time."

Elizabeth's breath caught in her throat. "W-what are you saying?"

John smiled and merely shook her head. "Nothing right now," he stated as he leaned in to whisper in her ear. "But know this hun; nothing is going to take me away from you- ever. I'm yours to keep."

* * *

A/N2) Hee, hee! Not quite a bad cliff-hanger, but a cliff-hanger none the less. I have to say though my beloved readers I am totally loving your reviews!

**Missysillivan** I'm so thrilled that you're thrilled about finding this story- I was depressed at the end of lifeline too and decided to set things right- hence the story. I hope you're liking the direction that I'm taking it. And to the rest of my beloved loyal reviewers, **charmed225**, **jasminesmommy**, **sparklyshimmer2010**, **saphiretwin369**, **momm2five**, **cocagirl2**, **whirlwind-2005**, **stargatesomeone**, **lantia4ever,** **Jean.DuVent**, **StormO, Serised** and all the rest- thank you for your reviews.

Thanks to you all my review count is almost at 100 and thank you to everyone who is simply reading this story because I have over 10 thousand hits. Totally overwhelming, and I want you to know that so long as Atlantis continues- this story shall continue as well- though I am thinking of changing the title to 'Elizabeth's Story' what do y'all think?

–Till next week. Anjirika


	15. Part I: Forever Mine

A/N- Okay gang. So like last week I haven't even seen 'Outcast' yet but I've read the transcript and while I've seen a whole TON of places to put our dear Lizzie- there are just a few that seem appropriate. So enjoy- and leave a review if you can. Oh- and I hope you enjoy my ending...

Forever Mine

"So tell me," Elizabeth began with a smile as they walked back to John's quarters. "Next time we watch a movie can I pick it?"

John looked at her as though she was insane. "Are you telling me that you didn't like Mission Impossible?"

"Oh I liked it well enough," Elizabeth answered as she hung onto John's arm. "But you know, it's like football I'll watch it with you because well- it's you. But I'd much rather watch a comedy- romantic if possible."

John just smiled as they reached the door to his quarters and he was just about to open it when Samantha ran up to them. "Colonel." She called out startling both John and Elizabeth. "Colonel I was just coming to see you." Sam paused as she saw Elizabeth beside him. "Uh- do you have a minute?"

"Uh yeah," John answered with a nod of his head. "What is it?"

"I just received a message from Stargate Command." Samantha began, her face looking tight and grim. "And I'm afraid that I have some bad news."

"Which is?"

"Your father suffered a heart attack last night," Sam explained watching as John's eyes widened. "I'm sorry John, but he passed away."

---sparky---

Less than three hours later, John was standing in front of the Stargate holding a plain duffle bag as the gate began to dial out. A thousand emotions were coursing through him and it wasn't until he felt a hand on his shoulder that he began to focus.

"John?" Elizabeth asked tentatively. "Are you going to be okay?"

Startled at Elizabeth's presence John took a look at his girlfriend and saw that she too had a duffle bag around her shoulder. "Are you going somewhere?"

Elizabeth glanced down at her bag and then back at John. "Yeah- with you."

"But you-"

"Yes," Elizabeth interrupted with a soft smile. "Yes I do. What kind of girlfriend would I be if I didn't go?"

John didn't say anything- he just nodded and took Elizabeth's hand leading her through the gate.

---sparky---

Elizabeth and John arrived in a small eastern-seaboard town and when they exited the car Elizabeth was amazed at how many people were milling about. "There sure are a lot of people here," she commented as she held onto John's arm.

"Yeah," John agreed with a small nod. "The old man was pretty well connected."

Elizabeth scanned the crowd and saw that one many was coming towards them. "Who's that?" she whispered quietly into John's ear.

"Brother," he whispered back- equally as quickly.

'Brother?' she thought her eyes wide as she watched the man come and stand before them. 'What other secrets does John hold?'

"John," the man before them stated curtly.

"Dave." John responded just as curtly.

"I wasn't sure you were gonna make it."

John shrugged and Dave extended his hand. With a single imperceptible nudge from Elizabeth John took his brother's hand and shook it.

"It's good to see you," Dave continued. "I contacted your unit commander at Peterson but sometimes those messages don't seem to reach you."

"Well I cam as soon as I heard." John answered trying to sound as nonchalant as possible. And he watched as Dave eyed Elizabeth and subtly tightened his arm around his girlfriend. "Dave, this is Elizabeth. Elizabeth this is my brother, Dave."

"Nice to meet you," Elizabeth said politely as she held out her hand.

"Yeah," Dave agreed, still eyeing Elizabeth. "Nice to meet you too," he paused and questioned the two of them. "You two work together in the Air Force?"

"I'm a diplomat." Elizabeth answered her 'negotiator' face on. "I work with the Air Force in consultation with our allies."

Dave eyed her suspiciously as if he didn't quite believe that Elizabeth could be a negotiator- but in a single look he averted his eyes and nodded. "Right- of course- anyway John I think that we should probably talk."

"Yeah," John agreed with a heavy sigh. "We probably should."

"Well I can't do it right now," Dave answered with an occupied look. "You know, so many people to talk to, thank them for being here..." he paused and looked straight at Elizabeth. "Thank you for being here...I'll catch up with you later John."

Without speaking John nodded and watched as Dave turned and left. Once he was out of earshot Elizabeth kissed John comfortingly on the cheek. "I can see why you never mentioned him. He's such a-"

"Jerk," John answered with a sigh. "But he's my brother and-"

"-and you don't have to like him John," Elizabeth answered quietly. "Despite what they say about not being able to choose your family..."

"I already chose my family." John answered as he began to pull Elizabeth towards the house. "And their all back home."

Elizabeth nodded in understanding and together they made their way into the house. They wound their way through the myriad of people until they found themselves in a large den where the closed casket belonging to John's father lay. There was a single portrait next to it and Elizabeth could see _Patrick_ inscribed on the small plaque

'Patrick,' she thought as gazed upon the harsh man in the photo. 'So that was your name...'

Once the few mourners had left the room, John nodded to them and slowly approached his father's casket self-consciously buttoning up his jacket as he got closer- something that did not escape Elizabeth's notice.

'Even though he's dead,' Elizabeth thought sadly 'John still can't help but look his very best.'

Elizabeth watched as John gazed down at the casket and then slowly walked up to him, placing one arm around his waist and another on his shoulder as she stood behind him. "He's in a better place now," she whispered. "He feels no pain."

"If only he could-" John whispered with a barley contained hatred that she had only heard on few occasions. "-I know that's poor of me to say because he was my father and all but Elizabeth you don't understand...no matter what I did, I could never measure up. I was never bright enough, never strong enough, never the good son. When I joined the military it was as much a chance to do something good with my life as it was a chance to get away from all this..."

"Oh John," Elizabeth whispered as she kissed him on his neck. "I am so sorry."

---sparky---

An hour or so later Elizabeth and John had wandered back out into the garden enjoying the fine spring air-despite the circumstances. "So," began Elizabeth slowly as she saw John's gaze fixed on the house. "Is this the house you grew up in?"

"One of them," John answered. "We moved around a lot."

"That must have been hard,"

John nodded. "Yeah it was. Never had a lot of time to make friends. Dad's business always taking us from one city to the next...couldn't wait to get out of here."

"Why?" asked Elizabeth completely curious about the side of John she never saw.

"My Dad's idea of teenage rebellion was going to Stanford instead of Harvard," John explained. "You can imagine how he reacted when I decided to go into the military."

"Why did you join the military John?" asked Elizabeth.

John shrugged. "Part of it was me rebelling against everything I had ever known, another was a need to do something good and I didn't see how being a lawyer like my grandfather or a businessman like my father would do me any good."

Elizabeth hugged John's arm a little tighter. "Well I for one and glad that you were such a rebel."

"Yeah," John agreed with a smile- the first in ages. "Me too."

Suddenly there was a laugh and Elizabeth and John looked up to see Dave talking and laughing with the minister and other mourners. "He seems friendly." Elizabeth said.

John nodded. "Yeah, that's what he does- friendly to a fault."

"So how come you never mentioned him before?" Elizabeth began remembering something from long ago. "And come to mention it, why didn't you let any of us know that you had a family- four years ago during the siege you said that-"

"That some of us don't have families back here," John interrupted. "And the truth is I didn't. When I joined the military I was ostracized. My Dad kicked me out and forbade me from ever coming to see him again. So I stayed away-" a bitter laugh forced its way from John's throat. "It was the one thing that he told me to do and I did."

John sighed and glanced back up at the crowd and saw a woman approaching him. She was wearing a simple black dress and John could feel an almost panic feeling settle in his stomach and her dropped his gaze. "Liz, I told you I had an ex-wife right?"

"Of course." Elizabeth answered. "You told me that months ago when we had that lovely conversation about how horrible ex's can be...why?"

"Here she comes."

Now it was Elizabeth's turn to be nervous.

"Hi John," the woman whom Elizabeth now knew to be Nancy said a warm smile on her face.

"Nancy," John replied. "I didn't expect to see you here."

Nancy reached out and enveloped John in a hug. "I am so sorry 'bout your Dad." she whispered and Elizabeth could feel her heart tightening. So she coughed to let the ex know that she was there. "Oh I am sorry," Nancy apologized looking at Elizabeth. "John's never been that good with introductions."

"Nancy this is Elizabeth my girlfriend. Elizabeth this is Nancy my ex-wife."

Nancy held out her hand to Elizabeth and of course Elizabeth being the diplomat took it but once it was done her hands were instantly back around John's arm.

"Nice to meet you." Nancy stated with a smile.

"Nice to meet you too." Elizabeth replied with an equally forced smile.

"So how do you know John?"

"Elizabeth is the diplomat assigned to the Air Forces where I'm based."

Nancy nodded. "And where is that exactly John? I've searched all over Washington for information about you and...nothing."

"It's classified." Elizabeth said with a knowing smirk.

"So how long are you here?" John asked breaking the tension.

"Just today. I have to go back-"

"To Homeland Security?" John interrupted.

Nancy nodded. "Yeah, just got promoted actually. I'm a director now."

"Congrats." John said honestly pleased. And after a few awkward seconds he continued on. "So...how's Greg?"

"Grant." Nancy corrected.

"Grant." John echoed. "How is he?"

"Oh you know same old same old." Nancy stated with an awkward shrug. "He would have come but he's trying a case in Phoenix."

"So he's a lawyer?" Elizabeth asked. "Like John's grandfather."

"Yes..." Nancy confirmed with a nod. "...just got put on a big case actually."

"Sound's like he's doing well."

Nancy nodded again. "Yeah he is..." she smiled awkwardly and then lowered her voice. "You know John- your dad has been very good to me all these years you should know that."

John nodded himself. "Well I'm sure that he thought that marrying you was the best thing I ever did."

"Well I don't know about that," Nancy interrupted biting her lower lip. "But I'm sure that he would be proud to see you now- a Lieutenant Colonel I here. Congrats."

"All thanks to Elizabeth here." John stated modestly, knowing all along that he would have never been promoted if Elizabeth hadn't stuck up for him.

"Really?" Nancy asked her eyebrow raising. "How'd you manage that."

"Oh you know," Elizabeth answered with a sly grin. "We diplomats have our ways."

"Of course." Nancy agreed with a small laugh. "Well I'm sure that Patrick would have loved to have met you. And I'm sure that he would have liked you."

"Yeah," John agreed as he wrapped his arm around Elizabeth's waist. "Dad probably would have liked you."

Nancy just saw the way that John looked at Elizabeth and despite that she was with Grant- she couldn't help but be a little jealous. "Well I have to get going," she said suddenly. "It's good to see you again John. Take care of yourself wherever you are."

"I watch his back." Elizabeth stated.

Nancy nodded curtly. "I'm sure you do. Nice to meet you Elizabeth."

"Nice to meet you too." Elizabeth said back as Nancy walked away and as soon as she was out of ear-shot she whirled on John. "Is it okay for me NOT to like her?"

John laughed. "Of course. I don't like her much either."

Elizabeth's expression hardened slightly. "But you did marry her."

John shrugged. "I was young and I thought I was in love..." he sighed and planted a surprising but soft kiss on Elizabeth's mouth. "...but it never felt right and now I know why- what you and me have- this is love."

"Yes," Elizabeth agreed with a smile as she wrapped her arms around him. "Yes it is love."

---sparky---

What started out as a simple wake turned out to be a mission and for Elizabeth as she ushered Ava Dixon to their car she couldn't help but wonder why the universe just wouldn't let them have a few moments of peace on Earth.

"John," Dave began as Elizabeth began to walk over. "I was thinking that we should probably-"

"Something has come up." John interrupted. "I have to go."

"It's Dad's wake."

"I know that." John answered not liking the disapproving tone that his brother had in his voice. "But this is work related."

"Oh." Dave stated irritably. "What is it? The top secret, national security type of thing?"

John nodded glancing at Elizabeth who was at his side. "Yeah, something like that."

"This is so typical of you you know."

"Why don't you say what's really on your mind Dave?" Elizabeth asked her tone cool and calculating like when she was negotiating against any foe. "Honestly now."

"I just want to know one thing John," Dave said looking at John. "What's your level of expectation here?"

"What are you talking about?"

"I mean are you going to challenge the will?" Dave asked not seeing the look of horror on his brothers face. "I mean I have no idea what it says of course but I think that I can guess."

"We haven't spoken in more then ten years and that's what you want to talk about?" John asked his eyes wide and his voice level with barely controlled rage. "You wanna talk about money?"

"That is why you're here isn't it?" Dave asked. "You've been gone a long time John. It's not so much of a stretch- especially with the pittance the military gives out."

John glared at him. "You've got nothing to worry 'bout." he spat before leaving.

"Who do you think you are?" Elizabeth asked as soon as John was out of ear-shot. "How could you accuse him of coming back for just the money? You had no right to say that to him. He came back not for the money but because his father your father has just died. And despite the fact that John hasn't kept in touch- I know for a fact that he is haunted by that fact and I also know that if John could ask for one thing- it would be to say goodbye."

"He said all that to you?" Dave asked sceptically.

"No." Elizabeth admitted her eyes never leaving Dave's. "But I know him."

"Yeah," Dave agreed with a nod. "I think you do... listen maybe I was out of line but you should let John know that if I got the wrong impression of him it's because he left. I stayed here and ran the business and looked after Dad while he was out playing soldier."

"You know nothing of what he does." Elizabeth whispered her voice holding a fury within it. "So don't you dare judge him because he puts his life on the line EVERY day and he stayed away because...well your father forbade him to ever come back it must have been what he wanted."

Dave shook his head. "No, no Dad was just angry that night." he sighed. "Tell John that Dad regretted what happened between the two of them, right up to the end..." he turned and began to walk away before turning back. "...and let him know that if he ever wants a heart-to-heart with his brother that my door is always open."

---sparky---

It was all over. John had gotten the information from Nancy much to Elizabeth's dismay the replicator had been dismantled much to Elizabeth's dismay as well and yet she and John were walking contently along a forest path. "He really said that?" John asked with a shocked look on his face. "He said that his door is always open?"

Elizabeth nodded. "Yes. He did. And he meant it."

John sighed and Elizabeth knew how conflicted he must be feeling.

"We have a few hours before we're scheduled to go back- do you want to-"

"Yes." John interrupted taking Elizabeth's hand suddenly. "But before we go there's something I have to ask you."

"Yes?" Elizabeth asked her voice hitching as John pulled out a small velvet ring box. "Yes...?"

"You mean you'll marry me?" John asked a smile on his face as he opened the box to reveal the single solitary diamond glittering on its golden band. "Will you be with me forever?"

Elizabeth- to stunned for words, with tears in her eyes flung her arms around John and held him tight. "Yes." she murmured. "Yes."


	16. Part I: Blessings and Curses

A/N- Okay so I haven't seen 'Trio' yet- but from what I can gather (not seeing the transcript) it had more to do with Rodney, Sam and Jennifer then the rest of the team- which is good 'cause our dear sparky couple is going in a different direction anyways. So- in my cannon we'll pretend that 'Trio' takes place at the same time as 'Outcast' and therefore when John and Elizabeth get back, everything is back to normal---whatever normal is on Atlantis.

As always, don't forget to review! Oh- and I can't believe I didn't notice! My reviews passed 100! -SQUEE- (hands out cyber cookies to readers) Thank you all!

Blessings and Curses

Elizabeth was on top of the moon. The man that she had loved for more than three years and had been dating for roughly four months had asked to marry him. And of course, Elizabeth had said yes. As if she could say no. 'I love him,' she thought dreamily to herself as they walked up the path to her mothers georgian home. 'And he loves me- which is more then I could have ever asked for.'

"Are you sure you want to do this?" John asked turning to Elizabeth who was staring at the door. "I mean it's you Mom."

Elizabeth smiled. "Hey now it's not like our relationship is strained or anything," she pointed out, holding onto John's arm a little tighter. "I'm just nervous that's all- I hadn't even gotten around to telling her that we were dating and-"

"And nothing," John interrupted by placing a swift kiss on Elizabeth's lips. "If my hard-ass brother could not only forgive me but like you in the same conversation then I'm sure that your mother will like me."

Elizabeth laughed and nodded. "Of course. I'm just being silly."

Then with a deep breath she raised her hand to the door and knocked.

"Why Elizabeth!" Elizabeth's mother Karen remarked as soon as she opened the door. "Elizabeth what a pleasant surprise."

"Hello mom" Elizabeth said as she took a step forward and gave her mother a hug. "I've missed you."

"I've missed you to," Karen Weir stated as she pulled her daughter back to look at her. "But I see that you've recovered quite nicely from your accident...what was it again Elizabeth? A road side bomb?" she asked as she ushered her daughter and her friend inside her home.

Elizabeth glanced nervously to John and then back to her mother. "Something like that."

"You must forgive me sir," Karen Weir began as she glanced at John while she closed the door.. "My daughter despite being a diplomat was never very good at introducing people. I'm Karen Weir and you must be the famous John Sheppard."

"You know who I am?" John asked taking the hand that Karen had offered.

"Of course." Karen remarked with a nod. "In the past two years Elizabeth had told me much of her friends- nothing specific of course. I understand that what my daughter does is classified but you Colonel Sheppard are mentioned in almost every letter...speaking of which-" Karen continued whirling on her daughter. "The last letter I got from you was months ago! Five months ago to be exact and you only told me that you were recovering fine. Why the delay?"

"Sorry mom," Elizabeth apologized as Karen let the two of them into the neatly furnished sitting room. "But I've been very busy."

"I can see that," Karen remarked with a gentle smile as she saw Elizabeth twisting the engagement ring around her finger. "So when's the wedding?"

"Mom-?"

Karen laughed. "Where you do think you get your intuition from my dear?" she asked with a smile. "I may be no diplomat but I'm not stupid. I can see the way that you two relate to each other and the way you look at each other...not to mention I can plainly see that ring on your finger." she smiled again and looked to her daughter. "So tell me, when is the wedding?"

"Well we uh- haven't quite decided on that yet." John spoke up as he took Elizabeth's hand. "We have to go back tomorrow and won't know when I'll be able to have leave again." John paused and looked at Elizabeth. "Of course Mrs. Wier we'll want to make it when we can get back to the states next."

"Well I should hope so." Karen remarked. "I want to see the wedding of my only child here where she grew up and not in some god-forsaken war-ridden country...but you've already decided to have it here when you get your next shore leave John and please- call me Karen- Mrs. Weir was my mother in law."

"Okay...Karen."

Elizabeth's mom smiled. "Now tell me darling," she continued. "How did this fine young man propose to you?"

---sparky---

Despite the fact that they had only extended their Earth time for a day both John and Elizabeth couldn't say no to a home cooked meal by Karen. And while John played with Sedge in the backyard, the mother and daughter duo began the preparations.

"He's a good man Elizabeth."

"I know," Elizabeth stated as she glanced out the window.

"And he loves you more than life itself I think."

"I know that too." Elizabeth agreed.

"And he would do anything for you," Karen continued. "Even lay down his life."

Elizabeth nodded stiffly her mind running over all the times that John had saved her. "I know that too Mom," she whispered quietly as she cut up the mushrooms for the salad. "I know it because he's proven that to me more times then I can count..." Elizabeth sighed and knew that she couldn't say much. "Where I'm stationed is—well it can be a dangerous place and John's saved me many times."

Karen nodded slowly understanding even if she didn't like the thought of her only daughter out in the world in a dangerous place. "Well then your Colonel Sheppard is in my debt," she stated with a smile as she looked at her daughter. "Not only has he saved you- but he makes you happy."

"More than life Mom."

Karen nodded. "I know the feeling. When your father and I got together it was if the entire world was open to us...there was nothing that we couldn't do..." she paused, the pain of her husband's passing still fresh in her heart despite the years. "But sill, John is a good man."

"Yes mom," Elizabeth agreed with a smile. "He is."

---sparky---

"You come back soon now," Karen called as her daughter and fiancée made their way down her path to the street where a simple black car was sitting. "And don't forget to send me all the details about the wedding!"

"Don't worry Karen!" John called back with a smile. "We'll keep you well informed and thank you for the lunch!"

Karen smiled. "Think nothing of it. Take care!"

"Bye Mom!" Elizabeth called out as John opened her door for her.

"Goodbye Elizabeth!" Karen stated waving back. 'And take care.'

---sparky---

John and Elizabeth walked into the Gateroom of Atlantis and saw that Richard Woolsey was waiting for them along with General Landry. "Sir," John remarked coming to attention. "What can we do for you?"

"You can go back to your post." Richard remarked coolly. "But I am afraid that Elizabeth will have to say here."

"What?" Elizabeth asked. "Why?"

"The IOA is reviewing all 'alien' personal of the Atlantis expedition about their viability to continue hey want to start with you." Richard explained simply.

"What?" Elizabeth exclaimed. "But I'm not an alien. I'm human. I was born her on Earth. I've grown up here gone to the finest schools and-"

"-and yet you are now half-replicator." Richard interrupted. "That makes you a threat."

"I thought that we already covered this," John asked stepping forward noticing the look of discomfort on General Landry's face. "Elizabeth gets to stay on Atlantis on the condition that she's not in control anymore. We've been doing that and everything has been working fine for the last seven months." John snapped thinking of how his world had changed in those seven months- what with Elizabeth becoming half-replicator and Teyla becoming pregnant and a host of other adventures. "I don't understand why you'd be doing this now."

"This is not just my decision Colonel," Richard remarked. "This is the collective decision for the entire IOA now General," he continued. "Would you please have your people escort Doctor Weir to an interrogation room."

"What?" Elizabeth cried as Landry nodded and two large marines came forward and stepped on either side of her. "No! General you can't do this."

"My hands are tied Elizabeth," he apologized softly. "Jones, Barnum take her away."

"No!" Elizabeth protested as she tried to fight her way out of the grasp of the two marines but despite her half-replicator genetics she could do nothing. Especially one they started to drag her out of the gateroom. "John!" she cried as John moved to go forward but Landry had another marine subdue him by holding his arms behind his back. "John, help me!"

"Elizabeth!" John called back as he struggled. "Don't give up. I'll fix this I promise."

"I trust you." Elizabeth stated with a nod as the door to the gateroom closed shut.

"You let her go." John demanded as the marine let him go. "Woosley you have no right-"

"Oh I have every right." Richard stated coldly. "Now, if you are not prepared to resume your duties then I can have two of Landry's men escort you to your own interrogation room."

That stopped John. "No." he replied with a scowl. "No I'll go back to Atlantis."

"Good." Richard stated with a nod. "General if you excuse me I have a prisoner to talk to."

"The nerve of that rat," John muttered as soon as the door to the gateroom had closed behind him. "I should have decked him."

Landry nodded. "I know how you feel but I'm afraid that for the moment there's nothing that you could have done or said to have changed his mind." he sighed and nodded for Walter to dial Atlantis. "You showed considerable restraint, I know for a fact that the old SG1 wasn't half as content when the IOA wanted to kill Daniel... friends have to stick together."

"But she's more then my friend General," John admitted quietly as the gate wooshed open. "She's my fiancée."

"Oh..." Landry stated with surprise. "...well that explains a lot- er- congrats Colonel."

"Thanks," John stated slowly as he made his way up the ramp. "Make sure that Woosley and the IOA don't go too hard on her General," John asked. "Please."

"I promise." Landry agreed. "Don't you worry about a thing."

"Oh I'll worry sir," John replied as he stopped mere inches from the event horizon. "I can't help but worrying 'bout her. I love her." And with that, John stepped through the gate leaving Elizabeth behind.


	17. Part I: Without Her

A/N- I know that the new episode hasn't aired yet but I had to have this little chapter here. Please review. Oh and I've changed parts of 'Trio' to suit my purpose... Enjoy!

Without Her. 

When John got back to Atlantis he was seething. Rodney was there at the gate waiting for him and he instantly saw that there was a problem. "Where's Elizabeth, Sheppard?" he asked watching John's face as it contorted with barely controlled rage. "John?" Rodney asked again, softer and less annoyed this time with a slight panic. "Where is she?"

"She's back on Earth," John muttered as he made his way out of the control room with Rodney following close behind.

"What?" Rodney asked in shock. "Why?"

"I need to talk to Carter before I talk to anyone else." John stated through gritted teeth.

"Oh well she's in the infirmary."

Barely indicating that he had heard him, John switched directions and headed towards the infirmary.

-sparky-

Once he got there he found Samantha on an infirmary bed reading a book. "What happened to you?"

Sam looked up and smiled. "Hello John. Welcome back."

"Not so much of a welcome," John muttered under his breath before asking again; "Thanks- what happened to you?"

Sam grimaced. "Well it began about two days ago..."

"_So which planet is this again?" Sam asked as she looked to Rodney and Jennifer as they stood in her office. _

"_M5V-801" Rodney answered. "The one with the frequent tremors."_

"_Not to mention," Jennifer continued. "an abnormally number of people with debilitating respirator problems."_

"_It's a mining planet." Rodney explained. "That's not that surprising."_

"_How long have you worked in the mines Rodney?" _

"_Get to the point guys." Sam interrupted. "Please."_

"_Well they're experiencing upwards of four tremors a day. My seismic teams concluded that the are where they built their settlement is dangerously unstable-"_

"_Not to mention my environmental air quality tests come out way into the red."_

_Rodney grimaced. "My analysis was enough thank you."_

"_Well obviously it wasn't enough for them." Jennifer pointed out. "Anyway- these people said they've experienced tremors for as long as they can remember."_

"_Yes," Rodney agreed. "And I'm pretty sure they've been breathing even longer so again- my problem trumps yours."_

"_This is not a contest." Sam pointed out. "Obviously they're living in a settlement that's not safe for habitation. You need to convince them to move to another part of the continent."_

"_We tried." Jennifer stated. "It's not working."_

"_Why not?"_

"_Apparently," Rodney explained. "Twenty years ago the Genii kind of took over the planet and employed them all as miners."_

"_Mining what?" Sam asked curiously. _

"_Haven't a clue," Rodney continued. "But whatever it was they cleaned out the deposits and left."_

_Sam tilted her head to the side in confusion. "So...?"_

"_So they think that we're like the Genii and they want their cut."_

"_Ah."_

"_They're willing to move," Jennifer pointed out. "But they've got a list of demands a mile and a half long."_

"_And negotiating with alien settlements isn't exactly what my speciality is." Rodney added. "If only Elizabeth were here."_

"_Yeah," Sam agreed. "If only...but she's back on Earth with John right now so we're going to have to do without."_

"_We were hoping if you had some time," Jennifer began "then maybe you'd be willing to come-"_

"_It would save us a lot of time in the back and forth." Rodney interrupted. _

_Sam nodded. "Okay. I'll free up my afternoon."_

"_Thanks Sam." _

"_You're welcome." Sam replied. "I'll meet the two of you at the Gate in one hour."_

_Rodney groaned. "Uh- I was rather hoping that you'd go by yourself and I wouldn't have to-"_

"_One hour."_

"So Rodney didn't want to get his hands dirty as usual." John stated. "What happened next?"

"We got stuck in a hole." Sam continued. "And to pass the time till our next check in we played a game."

"_Steve Carell or Stephen Colbert?" asked Jennifer. _

"_Oo!" Sam exclaimed. "Colbert I think."_

"_Carrel." answered Rodney. "But I would pick Jon Stewart over the both of them."_

"_Interesting." Sam murmured with fascination._

"_If I was forced to of course." Rodney added quickly. _

_Sam nodded. "Of course."_

"_Hey-" Jennifer interrupted. "Did you and Katie-er-"_

"_Things are kind of messed up." Rodney admitted. _

"_Why?" asked Jennifer. "What happened? I thought she was going to talk to you."_

"_Well see- wait." Rodney said. "What do you know?"_

"_I know that you were going to propose to her but then changed your mind cause your not ready." Jennifer answered._

"_H-how do you know that?" Rodney asked his eyes wide. _

_Jennifer laughed. "Girl's Friday Poker Games." she answered with a smile. "You learn a lot that way."_

"_I had no idea." Rodney muttered._

"_Niether did I," agreed Sam- who felt hurt. _

"_Oh- sorry ma'am." Jennifer apologized. "Next time we have a game-"_

_Sam laughed brushing away her feelings. "It's okay. I'm not much of a poker player."_

"_Still," Jennifer stated. "We should have asked you."_

"_Not to make this all about me or anything- but what about Katie?" asked Rodney. _

"_She was going to talk to you." Jennifer answered. "She thinks that you and her are ready for marriage and she wanted you to know that...didn't she?"_

_Rodney looked down guiltily. "Well she tried..." he admitted. "But I wouldn't listen...and now she's filed for a transfer back to Earth and everything..."_

_Sam sighed. "I can always deny it you know...once you talk to her of course."_

"_But I don't know if I can talk to her." Rodney stated. "Not after I've screwed everything up like always...she probably hates me."_

"_She doesn't hate you Rodney."_

"_Oh I'm sure she does." Rodney said with a sigh. "Maybe it's for the best. I mean- you know- she deserves to be with someone who isn't such an idiot where relationships are concerned."_

_Jennifer sighs. "What she deserves is to be with a nice guy- like you. She wants you Rodney. She doesn't hate you- she's just hurt."_

"_Oh and how do you know this?"_

"_I'm a girl for one thing," Jennifer answered. "And for another I'm her friend and I know this- and so should you."_

"So has Rodney talked to Katie?" John asked, Sam's story putting his mind at ease for a little while."

"I don't know." Sam admitted. "And Katie might have to fight Jennifer for Rodney's attention."

"What?" John asked wondering why Jennifer would be going after Rodney.

"Well you see- Rodney owes her a drink..."

-sparky-

Little did they know that Rodney and Jennifer had already talked about that. When Sam was having her leg set in a cast they had a little heart to heart.

"Looks good." Jennifer said to the medic who was bandaging Rodney's hands. "Okay, thank you."

The medic walked away and Rodney turned to Jennifer. "How's Sam?"

"She's going to be okay," Jennifer answered with a relieved sigh. "It's a clean break but still they're re-setting it and putting her into a cast which means she's gonna be on crutches for a few weeks or so but she's gonna be on crutches for a few weeks or so, but she's gonna be fine. How're you doing?"

"I'd like to take a bath in whatever magical ointment they just put on my hands," Rodney admitted honestly. "Because they're the only thing that doesn't hurt...it's not gonna scar is it?

Jennifer smiled. "Chicks dig scars."

"Not the chicks I dig."

"You're gonna be fine," Jennifer stated. "And thanks by the way."

"For what?"

"You saved my life." Jennifer pointed out. "If you'd let go..."

"Ah," Rodney interrupted. "You're welcome...right now well I'm going back to my room curling up in the foetal position and sleeping for the next three days."

"Oh well not quite yet." Jennifer stated jumping of the infirmary bed as well. "You owe me a beer from that bar trick thing earlier--- you couldn't figure it out so-"

"There was no time." Rodney insisted. "I would have figured it out."

Jennifer laughed. "Yeah well eventually chimps would have been able to figure it out but the thing is you didn't so I win and you owe me a beer."

"I don't remember ever agreeing to the beer." Rodney protested.

"McKay..."

"What?"

Jennifer smiled. "Do you wanna have a drink with me or not?"

Rodney just stared at Jennifer in shock. "What you want to have a drink with me? Like on a date?"

"No!" Jennifer replied half panicked half amused. "As a friend. You're not very good at having a girl for your friend are you?"

Rodney paused and thought about it—sure he knew lots of women but the ones that he did he usually carried a torch for- 'Like Sam,' he thought wistfully to himself. 'Though we're not friends...and then there's Elizabeth but she's John's and then there's Katie-'

"Rodney?" Jennifer asked interrupting his thoughts. "You're not good at this are you?"

Rodney shook his head. "No. I'm really not."

"Well then," Jennifer began with a smile. "Come on then..."

They were halfway out the door when Jennifer thought of something. "On second thought forget about owing me a drink- take Katie to the mess hall and let her talk to you. I think that your time would be better spent with her then me..."

-sparky-

"So who knows whether they've actually had the drink or not." finished Sam.

"For your information," interrupted Rodney. "Jennifer and I didn't have a drink-"

"Oh no?" John asked raising an eye brow as Rodney came into the infirmary. "Then who-?"

"Katie." Rodney interrupted again. "I had a drink with Katie and she explained everything and-"

"And?" Sam asked sitting up a little straighter.

Rodney smiled. "Well lets just say Atlantis is going to be hearing wedding bells in a couple of months---oh! That reminds me," he continued before either Sam or John could congratulate him. "Sheppard, what about you? Did Elizabeth..." he trailed off and looked around. "...actually where is she? You two have been glued at the hip lately and you didn't explain why she didn't come through the gate with you."

"Elizabeth didn't come back from Earth?" Sam asked noticing the dark look on John's face.

"No." He replied. "No she didn't."

"What?" Rodney asked. "Why not? Did she say no? Is that what it was? She didn't-"

"She said yes McKay." John snapped causing both Sam and Rodney to be taken aback. "She said yes but the IOA ambushed us at the gate and took her away."

"Wait a minute-" Sam began interrupting Rodney's incoherent muttering. "-what did Elizabeth say yet too?"

"I proposed." John stated quietly. "I proposed and she said yes and now she's stuck on Earth being interrogated by Woosley and I-"

"You mean you left her there?" Rodney asked. "How could you leave her there! I thought-"

"I know!" John snapped. "I know. But it was either come back without her or stay and be interrogated with her and I figured that I could do more here then there..."

That shut Rodney up.

"I think you made the right decision John," Sam said with a sympathetic nod. "And in the morning I'll call a meeting with the staff and we'll talk about what we're going to do."

_A/N- So here's the little in-between chapter. Hope you guys like! And I have to say that I'm so glad that you guys are reading and reviewing my version of season 4 within the basic cannon structure. I mean I hate the way the show is going but if I can make you guys happy while making myself happy then that's the best:D So please leave a review and lemme know what you think!_


	18. Part I: Proving Yourself

A/N- As always beloved readers- I haven't seen 'Midway' nor will I- or I might seeing how it seems to be an okay episode but I did see a lot of potential for conversion when I was reading the transcript. So please- read and review and enjoy! Oh- and sorry for the delay in uploading this but I wanted to see where 'The Kindred' went story line wise...and so I've updated this chapter plus two more...lemme know what you guys think!

Proving Yourself

Elizabeth was sick and tired of being stuck in the brig. The three grey walls were constantly seeming to be closing in and the bars that made up the fourth wall were mocking her. 'I don't understand it...' she thought bitterly to herself as she sat on her hard cot. 'I've all but given my life for Atlantis and this is how they treat me? This-'

"Dr. Wier?" interrupted a soft voice and Elizabeth looked up to see Vala, her hair in pigtails standing there with Daniel at her side. "Can we talk to you?"

"Of course Vala," Elizabeth said with a half-hearted smile as she rose and walked to the bars. "It's good to see you...and you too Daniel."

"Elizabeth." Daniel replied with a nod. "I'm so sorry for what they're putting you through- I hope that you understand that I-"

"Would fight them if you could?" asked Elizabeth, watching as Daniel nodded. "I know."

"I don't know if you do." Daniel replied softly. "I for one know about dealing with replicators-"

"I'm not a replicator."

"No one is saying that you are." Vala pointed out.

"Yes they are." Elizabeth insisted. "They wanted to pull me from Atlantis months ago but I fought them and the first minute that I step foot on Earth they snatch me."

"They just don't understand." Daniel continued. "They don't understand that replicators aren't that much different from us."

"Oh I don't know about that..." Elizabeth stated with a frown.

"They aren't." Daniel insisted. "I happen to know that their creator- at least their creator in our galaxy was capable of feelings and she was a pure android. You're still half human-"

"I'm all human." Elizabeth corrected. "I just have those little buggers keeping me together. I'd be dead if it weren't for them. I'm still me though."

"I know that..." Daniel said as he rubbed the bridge of his nose. "...all I'm saying is that if there is anything that you want us to do..."

"Can you contact Atlantis?" Elizabeth asked. "Can you ask them if John can accompany Teyla on her IOA visit here? I know that she's scheduled to come tomorrow and I was hoping that-"

"Of course." Vala agreed reaching between the bars to touch Elizabeth's hands. "We'll send that message...it will have to take some stealth however because General Landry has been monitoring all communications with Atlantis but still-"

"We'll do it Elizabeth." Daniel promised "I swear that we will."

-sparky-

Elizabeth woke with a start. The door to the brig was opening and as she sat up she saw her beloved John walk into her prison. "John?" Elizabeth asked tentatively as she gazed upon her fiancée who instantly was at the bars. "Is that you?"

"Of course it's me." John insisted as he reached through the bars to take her hand. "Who else were you expecting?"

"No one." Elizabeth answered as she took his hand and subsequently stood almost nose to nose with him. "I was just afraid that you were a dream."

"I'm no dream," he assured as he caressed her cheek the best that he could. "I'm here."

"And for that I am forever grateful."

"Are they treating you well?" John asked, momentarily glancing at her surroundings. "I mean are you going to be here long?"

"I don't know." Elizabeth admitted with a sigh. "I've been here ever since they dragged me away from you."

"You mean you haven't even been interrogated yet?"

She shook her head. "No. Not yet."

"This is so wrong..." John protested.

"I know."

"I mean you've done so much for Atlantis," he continued.

"I know."

"You've all but given your life to protect us all-"

"John!" Elizabeth interrupted. "I know. I know it- you know it- our family on Atlantis knows it."

"You just have to get these jerks to know it."

Elizabeth nodded. "Yeah- if they ever let me talk to them."

"Well no matter what happens," John began as he gripped Elizabeth's hand. "I'm not going to let you go without a fight- and you better not give up either."

"Oh I have no intention of letting them keep me here forever," Elizabeth promised. "I'm going to use all my negotiating skills to get myself out of here."

"Good." John stated with a small sigh. He glanced over his shoulder to the door and then brought his gaze back to his Elizabeth. "Listen-"

"You have to go." Elizabeth finished, a knowing look in her eye. "I know- I understand. I just wanted to see you."

"I won't give up," John promised in a hushed whisper and he brought his lips as close to Elizabeth as he could. "I'm going to get you out of here."

"Not if I get myself out of here first." Elizabeth stated with a smile. "But I can't ask you to get into trouble- so go."

"Elizabeth-"

"Go."

John sighed. "I love you, you know."

"I know." Elizabeth confirmed with nod. "I know it in every fibre of my being- just like I know that you have to go now or you'll be stuck in here with me."

"That wouldn't be the worst thing-"

Elizabeth laughed. "Go."

He nodded. "Okay, okay... I miss you."

"I miss you too."

And with that John was gone leaving Elizabeth alone once again.

-sparky-

Sam was waiting in her office when John and Teyla walked in. "Welcome back."

"Thank you." Teyla stated. "Believe me it is good to be back."

Both of them sat down across from Sam who just looked at them. "Did you see much of Earth?"

Teyla shook her head at Sam's question. "No. I saw nothing beyond the walls of Stargate Command for two days."

"And the interview?"

"It went exactly as you said it would Colonel Carter," Teyla explained. "The member of the IOA, Mr. Coolidge was somewhat brusque and arrogant. He insisted on doing most of the questioning himself."

Sam nodded. "I thought he would. The interviews were the first item on his agenda."

"Yes," Teyla agreed. "Well- he is clearly distrustful of aliens participating in any aspect of the Stargate programme, let alone being active team members."

"But you did change his mind," Sam asked. "Right?"

Teyla sighed. "I hope so, although he did seem distracted by my current condition."

"Really?" asked Sam. "I informed the IOA of your pregnancy as soon as your team knew."

"Yes the IOA knew," Teyla explained. "And while most of the members were quite supportive Mr. Coolidge- his demeanour toward women differs from his demeanour toward men. He kept calling me 'honey.' and while I admit that the urge to inflict harm on him was quite strong I somehow managed to refrain from doing so."

"That's probably a good thing," Sam agreed.

"In the end," Teyla continued. "I do not think that he will have a problem with me- mainly because I think he believes that I will not be returning to active duty once my son is born."

"Well, won't he be surprised." John muttered hardly noticing that while Teyla smiled at him her expression was one of doubt. He didn't notice because he was still mulling over the fact that he had only gotten to see Elizabeth the once and the whole prospect of losing Teyla as a part of his team made him slightly nauseous. He felt as though his entire world was falling apart- first Carson and then he almost lost Elizabeth and now he had for the time being and he wasn't prepared to lose Teyla either.

"Well," Sam began interrupted John's musings. "We'll cross that bridge when we come to it. In the meantime it's important that we get through these interviews as smoothly as possible and not create any waves..." she looked sympathetically at Teyla and nodded. "I'll inform you when the report comes in."

"Thank you Colonel Carter."

And with that Teyla was out of the room leaving John and Sam alone.

"Are you thinking what I'm thinking?" she asked.

John nodded. "First Elizabeth, now Teyla...Ronon's bound to be next. And that'll cause big waves- like Tsunami size...like first storm wise."

"First storm?" Sam asked before she remembered that just a few months after the Atlantis Expedition had set up in Atlantis a huge storm had nearly wiped them out. "Oh right- of course. Anyways, I've thought about that and while Ronon's interview isn't for three more days I've asked someone to come to Atlantis and coach him."

John looked interested. "Who?"

"Teal'c."

"Ah-" he replied. "Perfect choice."

"Speaking of perfect choices," Sam began. "How's Elizabeth?"

"Frustrated." John answered. "She's been stuck behind bars since I left the SGC the first time and she hadn't been interviewed by the time I was there."

"I don't understand what the IOA are waiting for." Sam stated as she leaned back in her chair. "I mean, Elizabeth had done nothing wrong."

"Except being turned into half-replicator." John pointed out bitterly.

"That's hardly her fault," Sam insisted. "I mean the nanites are saving her life. Without them she would have been dead...and with them she managed to provide you and your team with enough distraction to steal the ZPM which is now powering Atlantis in cases of emergency."

"I know," John agreed with a sigh. "She's given so much and they-"

"They don't understand." Sam interrupted. "They never have and they never will- not until they're out here. And you know what- that's something that Elizabeth had to learn too. When she first took over the SGC she was no better then any of the IOA personnel."

"I don't buy that." John argued.

"It's true-" Sam insisted. "Whether you choose to believe it or not it is true...and I'd hazard a guess that you had to teach her a few things about priorities and loyalties..." she paused and watched as John thought and he remembered how it wasn't until the end of the first year that Elizabeth really got it.

He sighed. "You're right. Of course you're right. Elizabeth's learnt what's important to us military people and hopefully she can make the IOA see that she's an asset not a threat."

-sparky-

'How quickly things spiral out of control-' Elizabeth thought as she saw the wraith opening her cell. 'They bring me here because they think that I'm a threat but the real threat made it here anyways'

"You will come with us," the wraith demanded as he pointed his stunner at her.

"I don't think so," Elizabeth replied taking a step further in to her cell.

"If you will not come," the wraith began his voice low and deadly. "Then you will die."

And before Elizabeth could react, the wraith was feeding.

-sparky-

John and his team stepped through to the midway station. "Ronon, Teal'c- come in." he waited a moment but there was no reply. "Ronon do you copy? And still there was no answer and while John was concerned about both Ronon and Teal'c he couldn't help but feel concerned about Elizabeth. And for the first time he realized that the wraith must have made it to Earth already and that she could be in some very real danger.

-sparky-

Ronon and Teal'c were searching the SGC for the wraith and along the way Ronon realized something. "Dr. Weir is here somewhere isn't she?"

"Indeed."

"Then we have to find her."

Teal'c nodded. "This way."

-sparky-

Both Ronon and Teal'c noticed right away that something was wrong. Elizabeth was lying face down on the floor of her cell- and the door was empty. "Dr. Weir!" Ronon stated as he rushed to her side fearing the worst and knowing that if she was dead that John would be as good as dead too. "Dr-"

Elizabeth groaned and rolled onto her back, and then she sat up with a gasp with her hand to her chest. "Oh God-" she muttered tears coming to her eyes.

"Dr. Weir?" asked Teal'c, brining her attention to them.

"Ronon, Teal'c-"

"Dr Weir what happened?" Ronon asked seeing how shaking up she was.

"He fed on me..." she replied in a shaky voice. "That bastard- the wraith- fed on me."

"And yet you are still here." Teal''c pointed out.

"He's right." Ronon agreed. "You're alive."

"I know," Elizabeth stated. "I don't know how- but believe me... I know."

"Well we don't have time to think about that now," Ronon explained. "There are wraith on the base and believe me you do not wanting them attacking your world."

Elizabeth nodded, "Can you get me a weapon?"

"Indeed."

Elizabeth smiled at Teal'c and allowed Ronon to help her to her feet. "Then let's go."

"And who else beside you are going after them?" asked Mr. Coolidge the man that Richard Woosley had sent to administer the interviews of both Teyla and Ronon.

"It's just the three of us," Elizabeth replied watching as the man's face fell.

"Get me a radio." he demanded. "Now."

Coolidge had gotten away and both Ronon and Elizabeth found him in the Control Room calling for help. "We don't have the time," he was explaining. "Now there's an excape hatch to the surface, we need to get to it immediately...Where's Teal'c?"

"In trouble," replied Elizabeth as she pointed to a video screen which showed Teal'c surrounded with wraith guards firing at him from either end of the hallway.

"He's surrounded." Ronon pointed out. "I need to get back to him,"

"No!" Coolidge complained. "We can't go back for him, we could get bogged down or killed!"

"You wanna run away and saver yourself then fine," Ronon replied as he turned and left.

"Dr. Weir-"

Elizabeth shook her head. "Teal'c is in trouble, and I'm going to help Ronon save him."

"Ronon Dex," Coolidge began as he sat in the centre of a five IOA member table across from Elizabeth and Ronon. "Do you feel that you can fulfil the duties of an SG team member with diligence, integrity and respect for those in authority over you?"

"Yes."

Coolidge looked to his colleagues and then back to Ronon. "Good enough for me."

"But-"

"Dr. Elizabeth Weir," Coolidge began again cutting Ronon off. "Do you feel that you can participate as a member of the Atlantis expedition without letting your replicator nature taking control?"

"As Dr. Keller's results have showed," Elizabeth began curtly. "I am no threat because my nanites serve one function- to keep me alive..." she paused and then thought of something. "...and there is the fact that the replicators are gone now so I can't get under their control again..."

Coolidge nodded. "Do you feel as though you can still make a valuable contribution to the team?"

Elizabeth nodded herself. "Aside from my vast knowledge and innate sense of how to handle a diplomatic situation, I am immune to the wraith and that could provide us with a great advantage."

Coolidge smiled. "Very well. You both are free to go."

Elizabeth looked at her sleeping fiancee and smiled. She leaned forward and kissed him gently on the temple causing him to jerk awake. For a moment he was stunned as though he was seeing a ghost- but then he realized that she was there, right beside him...and he couldn't believe it. "Elizabeth?" he asked as he sat up. "Is that really you? Are you really here?"

Elizabeth giggled and sat down in his lap. "Yup," she replied as she wrapped her hands around his neck. "It's me. I'm here."

"This isn't a dream?"

Elizabeth snook her head. "Nope."

"Oh thank god..." John muttered as he leaned into kiss her. He had his Elizabeth back- and he was never going to let her go.


	19. Part I: Lost Without You

Lost without You

"So you both passed?" John asked later that night as he and Elizabeth cuddled in his bed in his quarters upon the Daedalus. It was going to take a day or so to get back to Atlantis. "The IOA has accepted the two of you?"

Elizabeth nodded. "They thought that Ronon was the perfect man to have in the field- and they just plain out liked me."

"Well," John began with a knowing smile. "What's not to like?"

-sparky-

A few days after they arrived back at Atlantis, John was off searching for Todd and Elizabeth was helping Teyla search for her people. She was the only one who totally believed her and despite the fact that she and her team had visited this planet once before with no success, Elizabeth had convinced Sam into letting herself, Teyla go back so long as they were escorted by Lorne and his team. And this time, the visit had proved to be most useful.

"Listen Teyla..." Lorne continued as he walked beside Teyla with Elizabeth on her other side. "...I know that you're looking for answers to what happened to your people but I'm thinking that maybe it'll be better if you let us check it out okay?"

"Major," Teyla began warningly.

"He's only suggesting that they scout ahead," Elizabeth pointed out and she could see that Elizabeth was about to agree when suddenly a faint but familar whining sound was heard in the sky. "What's that?" Elizabeth asked as she raised her head to the sky.

"A dart!" Teyla exclaimed. It was heading straight for them and while Lorne's team scattered Elizabeth tried to push Teyla out of the way but instead they both got beamed up.

'Oh god...' Lorne thought to himself as he watched the dart soar into the sky. '...this isn't good.'

-sparky-

"So when you put it that way," John pointed out at the end of Rodney's long explanation. "Giving them our research could be a good thing."

At that moment the Stargate began to dial in and they heard Chuck in the control room announcing the incoming wormhole. Samantha, John, Ronon and Rodney left the office and made their way down the stairs just as Lorne and his men came through. It shut down behind them and John watched the horror and guilt on the major's face and his stomach dropped.

"Major?" Sam asked as she stood in front of Lorne. "Where's Teyla and Elizabeth?"

"They-" Lorne began as he raised his head. "-they got captured by a dart."

"They what?!" John exclaimed in horror. "What?"

"We went back to the planet," Lorne explained. "We found a lead. We were going to dial in when a dart scooped them both up... though I'm pretty sure that Teyla was the intended target since the beam followed the two of them when Elizabeth pushed her out of the way."

"How could you let this happen?" John yelled as he took a threatening step towards Lorne.

"Colonel," Sam began warningly and she could see John calm down- barely.

"We need a plan." John stated suddenly whirling to face Sam. "We have to go after them."

Sam nodded. "I agree. But you're going to need help..."

-sparky-

Todd had given his help just as they had asked and now John's team minus Teyla and Lorne's team were searching a complex that began to Micheal and they had just taken their first prisoner. "Where's your boss?" John asked threateningly. "Hmm?"

"You're too early." the man replied.

"And what the hell does that mean?" John asked more to himself then to everyone else.

"We're expecting him back," the guard replied. "He's on his way with two important prisoners."

John's eyes widened and he contacted the Daedalus instantly.

-sparky-

"Bad news Sheppard," Caldwell stated over the radio. "The cruiser made the jump to hyperspace...it's gone."

"No!" John cried as he slammed his fist against the concrete wall. He had been so close to getting the two most important women in his life back. Elizabeth was the love of his life and Teyla was his dearest friend- and they were gone. They needed a new plan- but John didn't know where to go next.

He was lost without Elizabeth- and it frightened him. He had barely been able to function when she had been stuck at the SGC but now that she was out in the universe with Micheal of all beings and that frightened him.

"We'll find her..." Rodney promised as he stepped up to his best friend. "...she's out there."

"She's out there alright," John muttered as he looked Rodney in the eye. "Both her and Teyla are. They're our family and for as long as there's a chance to find them—we're going to keep trying."


	20. Part I: Found and Lost

Found and Lost

John's world had been turned upside down. Elizabeth and Teyla were still missing- but Carson or at least a being who looked like him was sitting in an isolation room on Atlantis. "It's just weird" Ronon remarked as they stared down at him. "I mean he's gone."

"I know," John replied his arms on the railing. "Are you sure he's not a replicator?"

"No," Rodney confirmed. "The scanners would have picked it up."

"Then what the hell is he?" asked John.

"Well I don't know," Rodney replied. "I mean I'm just as freaked out about this as you are."

John sighed and moved his shoulders uncomfortably. "You don't really think it's him do you?"

"No," Rodney stated but then his mind started moving. "Well I mean- maybe."

Both Ronon and John just looked at him and Rodney sighed. "Look we've ruled out advanced robotics that still leaves us with about half a dozen alternate explainations."

"Like?" Ronon asked.

"Like alternate timelines, parallel universe, cloining I mean take your pick.

"Just another day in outer space," John muttered as his eyes remained fixed on Carson.

"Yeah..." Rodney agreed as Jennifer came into the room.

"Well," she began with a sigh. "We've completed the preliminary tests."

"And?" Rodney asked.

"Every test we've run confirmed it, that man down there is Carson Beckett."

-sparky-

Elizabeth was in an empty cell. There was no sign of Micheal or Teyla or anyone else for that matter. She was being left alone and the hunger was starting to gnaw at her. 'I have to get out of here soon.' she thought desperatly to herself. 'I have to get back to John...but how?'

But Elizabeth had no answers and for the time being she could do nothing but sit and wait.

-sparky-

"Rodney-" Carson stated as his best friend came into the room.

"Carson- so sorry I haven't come by before now things have been a little hectic."

"That's okay I understand ..any word on when I can get out of here?" Carson asked hopefully.

"That might take a little time." Rodney stated with a sigh.

"Oh really..."

"...it's good to see you." Rodney muttered as he reached his hand out to shake Carson's hand

"Think about how I feel." Carson pointed out. "I'm the one who's been in prison for almost two years."

"Two years?'" asked Rodney.

"Aye- since MG8352- the planet where we left Micheal and the other converted wraith."

"Right- where you were captured"

"Well yes- you do remember Rodney?" Carson asked, thinking that Rodney was acting odd.

"Yes- we uh- just need you to fill in some of the details..."

And so Carson explained. Everything- about being captured about watching a poor woman being killed in front of his eyes and how he cooperated with combining wraith and human DNA. "Carson I'm I'm so sorry," Rodney murmured totally shocked at the vileness of Micheal.

"It wasn't easy, I'll admit at times I almost gave up hope- but that's when I thought about you, Colonel Sheppard, Teyla and the rest of the team...I knew you'd be out there somewhere looking for me."

"Yeah...see...the thing is we weren't" Rodney explained, knowing that he had to tell him.

"Weren't what?"

"Weren't looking for you- we didn't even know you were missing."

"Scuse me?" Carson asked not believing what he was hearing.

And so Rodney explained. About brining Carson back- another Carson Beckett back to Atlantis and how things had returned to normal and then how six months later how he had died in an explosion. The horror on Carson's face- or at least the Carson before Rodney was heartbreaking. "To us you weren't missing Carson, you were dead."

"I know this is a lot for you to take in," Rodney stated a few moments later.

"Aye," Carson agreed his hand over his mouth. "You're damn right it is. First you tell me I'm not the only Carson Beckett and then you tell me that the other one died in a horrible explosion..." and that's when it hit him. "Oh my god..." he exclaimed. "My mother...you didn't tell her did you?"

"Well- yeah." Rodney confirmed.

"Good Lord-" Carson muttered in horror.

"You were dead-" Rodney defended. "I mean I'm sorry to be blunt but we buried you there was a memorial service and her church I was there."

"This can't be happening I have to get back there I have to talk to her." Carson stated as he stood

"What?" Rodney asked as he stood up as well. "You can't. Do you have any idea what kinda effect that will have? I mean besides what are you going to say to her?"

"I'll say the airforce made a bloody mistake, that's what I'll say." Carson answered angrily.

"Carson "

"No Rodney this is too much get Elizabeth in here I need to speak to her right now...What?"

"Can't do that" Rodney stated quietly.

"Why not?"

"She's been captured Carson...by Micheal with Teyla. That's how we found you- looking for her- I'm sorry..." Rodney apologized as Rodney sunk to the chair again. "I don't know what to say."

"You know for the better part of two years I imagined what it woul dbe like when I finally got back to Atlantis...this isn't exactly how I pictured it."

"I know what you mean."

-sparky-

Teyla and Elizabeth were together again- finally. But they were on an unknown planet meeting an uncertain fate. "What is this place?" asked Teyla

"Just another dead world." Micheal explained. "Destroyed by the wraith, abandoned by the survivors, forgotten by both – a perfect place to conduct my work."

"And what was that?" asked Elizabeth.

"You will see." Micheal assured.

-sparky-

They were led inside and Micheal took them straight to a cell. "Open it." he stated and both Elizabeth and Teyla were ushered inside with Micheal saying; "I'll leave you to get reacquainted"

"Teyla?" asked a voice from above.

"Halling?" Teyla asked her eyes searching for the face.

"Dr. Weir!" exclaimed another voice that Elizabeth recognized.

"Jinto!" she exclaimed as she took Jinto in her arms.

They had found the Athosians- what was left of them anyways.

-sparky-

"I did not ever think that I would see you again." Teyla muttered as she, Halling, Elizabeth and Caene sat together.

"Nor did we," Halling "I just wish that it had been under different circumstances."

"We've all been so worried." Elizabeth stated. "We've never stopped looking."

"Were are the rest of our people?" asked Teyla fearing the worst.

And so Halling and Caene told Teyla and Elizabeth what had happened. How so many had been taken and changed... including Kanann and how he had been among the first. They explained how they had been ambushed and Teyla just sat there and listened with a heavy heart and at the end both she and Elizabeth assured them that Atlantis would be searching for them. But Caene stated how they themselves had held out the same hope until that very day- indicating without saying that it could be a very long time before they were rescued.

-sparky-

It was days later when Teyla was taken. Both Halling and Elizabeth tried to stop them but both were knocked to the ground. And in the end they could only watch as their friend was taken. "I'm sorry," Elizabeth apologized to Halling. "I tried to stop them."

"As did I..." Halling agreed. "But there was nothing we could do."

"We just have to wait," Elizabeth stated. "We have to wait and be patient. John and his team will be here soon," she reassured although that that moment she wasn't sure if she was reasurring herself or Halling more. "I know it..."

"I believe you..." Halling sighed. "...you speak of Colonel Sheppard with a tenderness that I have not heard in your voice before. What has happened?"

"He's my- we're well—we're engaged." Elizabeth explained, and upon seeing the confusion on Halling's face she clarified. "We're betrothed."

"Then my congratulations to you," Halling stated. "I can only hope that you get to see him again."

"I will." Elizabeth stated definitely trying to assure herself this time.. "I will... I know I will..."

-sparky-

Mere hours later there were gunshots which caused both Elizabeth and Halling to race to the bars of their cell. "Hello!?" Halling called once the gun shots had stopped. "Hello is anyone there? You myst help us."

There was silence...but then a voice answered. "Halling?"

"John!" Elizabeth cried out. "Through here!"

"Elizabeth!" John exclaimed and soon he was racing towards the sound of his fiancee's voice. He found her then at the bars with Halling.

"Colonel Sheppard," Halling stated with a smile. "It is very good to see you."

"Like wise," John replied, slighly out of breath as he turned to Elizabeth. "Elizabeth-"

"I'm okay," she assured as Ronon opened the cell door.

"Are you sure you're alright?" Carson asked again causing Elizabeth's eyes to widen. "Lass?"

"Carson!?" Elizabeth asked.

"Aye lass."

"But you're- you-" she could hardly say it- and a part of her almost believed that he hadn't died.

"It's a long story," Carson stated with a sigh.

"We'll explain it to you later." Rodney assured. "But is everyone alright?"

"We are," Halling assured. "those of us who are left...Teyla said that you would come."

"Where is she?" John asked. "Where's Teyla?"

"She was taken by Micheal." Elizabeth stated. "You guys have to go after her."

"Will you-"

"-I'll take care of the Athosians. I swear." Elizabeth finished as she clung to him

"We'll meet you at the gate." John stated as Elizabeth pulled away.

"Promise?" Elizabeth asked catching his eyes.

"Promise."

-sparky-

They had lost Teyla- again...and now they were losing Carson as well. The stasis chamber was all set up and all that was left was the final goodbyes. Carson was wheeled in by Keller and they watched as she assured him that she would fix things and that their best people were on it.

"And I've got Daniel searching through the Asgard database," Sam added. "I mean they cured the clone of Jack so maybe there will be something there—-but it will take some time. The data base is vast and not all that specific..."

"Either way we'll get the cure-" John promised. "Just as soon as we capture Micheal."

Then Carson went to each of them- he told Samantha about a letter for his mother and how in it were thoughts he should have said long ago. He then turned to John who promised that he would have him out of there soon. Carson in turn made him promise to bring Teyla home—he was wracked with guilt about being under Micheal's influence and making John swear to bring her home was the only thing that made him feel nominally better.

Carson then turned to Ronon who was very uncomfortable because he had been afraid about saying goodbye to him the entire time. But in the end, Ronon bent down for a hug. Carson then wen to Elizabeth.

"Elizabeth-"

"God Carson..." Elizabeth began with a tear in her eye. "I don't know what to say."

"You don't have to say anything lass...you've said enough on my behalf...Rodney told me what you said and I wanted to thank you- even though it wasn't me you were talking about."

"For the last time Carson it was you," Elizabeth stated. "You have to accept that you are you and it doesn't matter if you're a clone or not...I mean look at me."

"Aye...I guess we've both gone though some changes haven't we..."

"We have..." Elizabeth agreed. "...no matter what happens," she told him as she hugged him. "It was good to have you back- even for a little while."

"Aye..." Carson agreed as he turned to Rodney who then began babbling on out of nervousness. He stepped into the pod and just looked out at his friends. "Thank you Rodney, I want you all to know that seeing you again these last few days...it was all worth it no matter what happens..."

Rodney startled mumbling about dreams and the highlands and Carson who felt himself fading away just shook his head slowly. "Rodney- I'll be fine."

"That' right- you will be because this is not good bye this is this is see you later. It's what we agreed."

"Is it?" asked Carson, doubt still in his voice.

"It's how I remember it."

"Alright then...see you all later."

And then that was that- Carson was frozen and none of them knew if they'd ever be able to awaken him again.


	21. Part I: Future's Past

_A/N) So I have to say this, 'The Last Man' quite possibly has to be the BEST Stargate episode that I have EVER watched and that includes the Sparky favourites like 'The Storm/ The Eye' and 'Echoes' and 'The Real World' and 'Common Ground' and 'The Seige I-III' and well 'Lifeline' and 'This Mortal Coil' and so without further adieu here's the last instalment for now…_

Future's Past

"Okay Colonel Sheppard," Sam began as John and Lorne's team stood ready at the gate. "Good luck."

"Thanks-"

"John wait!" Elizabeth cried out as she came running to him.

"Elizabeth?"

Elizabeth smiled and gave her fiancée a huge hug and kiss. "Come back in one piece alright? With Teyla hopefully…."

John smiled. "Don't worry. I'll be back before you know it…."

-sparky-

"What do you mean he hasn't come back yet?" Lorne asked as the rest of his team came back through the wormhole. "He stepped back through hours ago."

"No." Elizabeth stated her arms crossed in front of her chest. "He didn't."

"But he did," Lorne insisted. "I was there."

"And I was here," Elizabeth stated angrily. "Now I am telling you Major Lorne that John did not come through that gate."

"Then where is he?" asked Rodney. And all who were there in the Gateroom; Lorne, Samantha, Rodney, Ronon and Elizabeth all looked at each other wondering what could have happened to him.

-sparky-

_Forty-Eight Thousand Years Later..._

She sat on the stairs leading down to the gate with her head in her hands. She had been waiting there for a long time- far too long but she didn't have a choice. The man she loved was out there and she was one of the only ones who could be there to great him. And so twenty-five years after his disappearance when Rodney and her had come back through they had set to work….and she had been waiting ever since.

Suddenly, the gate wooshed open and she was instantly on her feet her eyes wide with expectations. And then John came through- looking just as he had when he had disappeared in the freak accident.

"Elizabeth?" John asked as she came down the stairs and he looked around at the warm and slightly orange tainted control room. "What's going on?"

But Elizabeth couldn't speak- she couldn't trust her voice to work. Instead she just threw her arms around him and sobbed, although no tears came out of her eyes for after all- replicators can't cry.

-sparky-

Elizabeth finally calmed down enough to let John lead her to the steps and they both sat down. "Elizabeth," John began again. "What's going on?"

"It's been so long…" Elizabeth whispered as she traced the outline of his jaw. "…too long."

"Elizabeth it's only been about four hours since I left Atlantis,"

Elizabeth shook her head. "No."

"What do you mean no?"

"John…" Elizabeth began as she took him by the hand. "I have to show you something…."

-sparky-

John was in shock. Between Elizabeth and the Hologram of McKay he was briefed on what had happened. Forty-Eight Thousand years had gone by; Ronon had died blowing up one of Michael's facility, Sam had died aboard her ship 'The Phoenix' while Carson had never made it out of the stasis pod and Dr. Keller had died on Earth though repeated exposure to the Hoffin drug, Teyla had been killed by Michael and Elizabeth-

"You're a replicator?" asked John in shock.

Elizabeth nodded as they walked towards the stasis pod. "Rodney came up with the plan four days after Jennifer died. He knew that his plan might never be conceptualized and he figured that so long as one of us was around…"

"Forty-eight thousand years…"

"I know," Elizabeth sighed. "I told you that you were gone a long time…"

"I am sooo sorry," John apologized as he stopped dead in the hallway. "I mean-"

"John it's not your fault," Elizabeth assured as she took him by the hand and kissed him swiftly. "It was a freak accident like Rodney said. At least now we have a way to fix it."

John nodded and they continued walking. "I'm surprised that these corridors haven't filled with sand."

Elizabeth smiled. "Yeah well I knew that it was going to be a while till you came home so I kept busy. Most of the city is in good repair, there's just no power save for the Mark 12 that is keeping the hologram of Rodney going…"

"And for that I am ever grateful," answered Rodney as he materialized out of thin air. "But we need to get John into the pod quickly…"

-sparky-

"I hate goodbyes-" John muttered as Elizabeth set up what needed to be set up.

"I know," Elizabeth agreed softly. "But at least if this works-"

"If-?"

"When," Elizabeth corrected. "When this works none of this will have ever happened. You can stop Michael, save Teyla-"

"Marry you-"

Elizabeth smiled. "Marry me…"

"And live happily ever after." John finished.

Elizabeth shook her head. "I don't believe in happily ever afters…" she stated quietly. "Not anymore…"

John didn't say a word, he couldn't. He just took his fiancée into his arms and kissed her passionately. "I will fix this," John promised as Elizabeth buried her head in his neck. "I swear that I'll fix this…and we will have our happily ever after Elizabeth…I promise."

Elizabeth smiled into John's shoulder. "I believe you…."

-sparky-

"_Incoming wormhole…"_

"_It's Colonel Sheppard's IDC…"_

"_How long have I been gone…"_

"_Twelve days…"_

"_Twelve days…twelve days… I hate to say this but we're on the clock…"_

-sparky-

"So this time actually be back on time…" Elizabeth stated with a cheeky grin as John and his team suited up. "…I don't want to go- how long was it?"

"Uh Forty-eight thousand years-" Rodney answered looking at John. "Right?"

John nodded. "Give or take…"

Elizabeth sighed. "Okay- so I don't want to go almost fifty thousand years without seeing you, 'kay?"

"Kay-" John agreed as he gave Elizabeth a last kiss. "-let's go save Teyla…" he stated to the rest of his team including Lorne's men as they travelled through the gate.

"They'll be fine…" Samantha assured as the wormhole closed behind them.

"I know," Elizabeth agreed as they turned to walk away. "But do you ever get the feeling that something horrible is going to happen?"

Samantha smiled, "Every day of my life Elizabeth, every day of my life."

-sparky-

_"We have to get out of here now…."_

But it was too late- the building was coming down around them.

**A/N2) Well here we are gang- the end of the season...with number five on the horizon. There are changes in the air in the canon series and will be matching those changes blow for blow with one obvious exception...our dear Elizabeth isn't going any where. :D So please take the time to review this chapter because it will be the last one till at least July :P I hope you guys have enjoyed 'What Would Elizabeth Do' as much as I have...and so you know, when season five starts I'll be starting with a new story- so keep your eyes open! And thank you all for your amazing reviews! I'm glad you all liked my alternate version of Season 4 as much as I enjoyed writing it. :D**


	22. Part II: Searching

_A/N- Okay so Season 5 Episode 1 'Search and Rescue' totally got leaked and I'm so thrilled because not only was the episode fantastic but I'm able to get back to you all! I hope that you guys like this interpretation, I know that I do. And just so you guys know- this was a great chapter to convert and therefore I've had to split it up into two chapters because it was so long..._

**Chapter One: Searching **

--

"They'll be fine," Samantha assured as the wormhole closed behind them.

"I know," Elizabeth agreed as they turned to walk away. "But do you ever get the sense that something horrible is going to happen?"

Samantha smiled, "Everyday of my life Elizabeth, every day of my life."

Elizabeth shook her head. "Is that supposed to comfort me?"

"No," Samantha admitted as they walked up the staircase to the control room. "But what else can I say?"

Elizabeth paused and turned back to look at the dormant stargate. "Tell me that they'll be alright. Tell me that they'll find Teyla and everything will go back to normal."

Samantha nodded and placed a comforting hand on Elizabeth's shoulder. "Everything is going to be alright. John and his team are going to find Teyla. They'll bring her back here and everything will be back to normal…" she paused and noticed that Elizabeth wasn't convinced. "…not doing a good job, right?"

Elizabeth sighed and sat down on the stairs watching the stargate. "I don't know what to say," she whispered quietly. "Something's wrong, really wrong. I can't explain it but I can feel it."

Samantha nodded again. "Your spidey sense is tingling."

"I guess it is," Elizabeth agreed. "Is that a bad thing?"

"No," Samantha responded. "It just means that you have to trust your team. Trust John. He's gone on rescue missions before."

Elizabeth sighed. "I know. It's just I still can't help wondering…and worrying…" And with that Elizabeth Weir, former head of Atlantis and fiancée to one Lieutenant Colonel John Sheppard sat and stared at the stargate waiting, worrying and wondering if the love of her life was alright.

-sparky-

The mess hall was empty save for one table and many, many candles. At the table were comrades, teammates, friends and lovers. They were having a late night celebration and they were all enjoying themselves. "This is perfect," began John as he held up his wine glass with Elizabeth at his side. "Just what I needed."

Teyla nodded in agreement. "Truly it has been a hectic couple of weeks."

Rodney snorted at the irony. "Try four years," he muttered. "I mean after all we've gone through…I'm surprised I'm still standing."

"Now Rodney…" chastised Katie Brown as she kissed her fiancée on the cheek.

Teyla smiled. "He is right…" she defended, flashing the scientist a warm smile. "In a way it makes these calmer moments even more special." Teyla paused and looked at everyone. Ronan was staring at her intently, as were Samantha Carter, Elizabeth, John, Rodney, Jennifer and Katie. "I cherish these times," she continued with a warm smile. "When it is just us all enjoying ourselves, I am reminded of how blessed I am. You are like my family now, and for that I will be forever grateful."

Elizabeth nodded and raised her glass. "Here, here."

The rest of the party agreed and raised their glasses. John alone felt a little uneasy and he turned to look at Teyla. "You've got an early morning and I-"

"I never got to properly thank you," Teyla interrupted.

"Thank me?" asked John. "For what?"

"For what?" asked Teyla herself with a smile as though she knew something that John did not. "For rescuing me, from Michael- I never gave up hope because I knew. I knew that you would come for me John."

John shifted uneasily. "I know this sounds crazy," he began quietly, his voice hoarse and raspy. "But I don't remember rescuing you…"

"…you don't remember rescuing her because you didn't," interrupted the voice of Aiden Ford. John blinked and suddenly everyone was gone. "You didn't rescue Teyla just like you never rescued me," continued Aiden with a sad and heartbroken look on his face. "…or Elizabeth."

John shook his head. "No," he stated firmly. "No I tried to rescue you but you gave up your life to let me and my team go…and I did rescue Elizabeth. She's fine on Atlantis and-" and suddenly John stopped talking mid-sentence. There was a great pain in his lower abdomen and when he looked down he saw blood seeping through his white dress-shirt.

-sparky-

John jolted awake and was welcomed with searing pain all over his body. "Hey buddy," Ronan stated as he looked over his friend and leader.

"What happened?" asked John trying to make sense of the jumbled memories.

"Michael's compound," he answered. "It collapsed on us."

John tried to move but couldn't and winced in pain due to the effort. "Hey…" Ronan warned as he tried to stop John from moving.

"I think," John began trying to move away from the source of his pain. "I think,"

"Yeah, yeah," muttered Ronan. "Let me take a look." Ronan looked at John's side and saw a metal spike protruding from it. Taking a deep breath himself and not giving John a moment's notice he pulled it out, causing John to wince in pain.

"What the hell was that?" asked John with pain in his voice.

"That?" asked Ronan. "That was just a little scrape. No big deal."

John nodded weakly. "What about the others?"

"I dunno," Ronan admitted. "We got separated."

"Try them on the radio…" John suggested.

That? Just a little scrape, no big deal.

Ronan shook his head. "Already tried. I couldn't get through."

John winced. "There must be too much interference."

"Must be…" he agreed, noticing John's pained expression. "You okay?"

"Yeah, I'm fine."

"But?" asked Ronan not believing John at all.

"But nothing," John stated. "Except that Elizabeth is going to be so pissed."

-sparky-

Back at Atlantis it was the dead of night and Elizabeth was still staring at the gate when it suddenly wooshed to life. "Unscheduled off world Activation," said the voice of the female technician. "It's Lt. Edisons IDC."

Elizabeth was instantly walking down the steps to the gate with Samantha at her side. Both were shocked when Lt. Edison came through covered in dust and a bit of blood. "What happened?" asked Samantha finding her voice first. "Where's the rest of your team?"

"There was a massive explosion," answered Edison not even noticing how Elizabeth's face paled at the news. "Everyone was in the main compound, the whole building imploded on itself…"

"Where there any survivors?" asked Elizabeth finding her voice at last.

Edison shook his head. "Radios are down uh- I don't know. I just thought that I should get back here and-"

"No," interrupted Samantha with an understanding tone in her voice, "You did the right thing…." she paused and turned to one of the soldiers that was posted in the gateroom checking the cargo that had just been beamed down by the Daedalus. "Get him to the infirmary."

The soldier nodded and escorted Edison away. "How far away is the Daedalus?" asked Elizabeth, panic creeping into her voice.

"Still two hours out," answered Samantha as she placed her hands on her hips.

"We can't wait that long," Elizabeth stated her eyes wide. "They can't wait that long…."

Samantha nodded. "I know," she paused and turned to another young captain what was awaiting orders. "Have the combat engineers gear up and have Dr. Keller ready her away team."

"Yes ma'am," the captain stated as she turned and left leaving Elizabeth to face Samantha.

"Some spidey sense," Samantha muttered.

Elizabeth strained a smile. "I know. Pretty good isn't it?"

"We'll find them…" Samantha assured.

Elizabeth nodded. "Damn straight we will. I'm coming with you."

-sparky-

When they arrived on the scene it looked like a war zone. There were chunks of debris made of concrete and steel everywhere. Wherever Elizabeth stepped she was careful to listen. No life signs had popped up yet but she was still holding onto a shred of hope, despite what her eyes were seeing. _John's still alive…_ she told herself firmly as they continued walking. _He has to be…I'd know it if he wasn't_.

"Right," stated Sam her voice cutting through Elizabeth's thoughts. "We've got four life signs in two different locations."

_Thank god…_ thought Elizabeth to herself as she closed her eyes and gave a silent prayer of thanks.

"The first two should be right beneath us," continued Sam as she searched the ground hoping for an answer. Jennifer in the meantime suddenly stopped. "Listen," she whispered and Elizabeth looked at the young doctor while straining her own ears. There were sounds coming from beneath their feet. They were muffled, yet they did sound like two male voices calling for help. Elizabeth watched as a young female soldier bent down to a crack in the debris and listened closely herself.

"McKay?" called Samantha. "Is that you?"

"Oh thank god," came the muffled reply causing a piece of Elizabeth's heart to soar with hope as she imagined her John being right there with Rodney. "Yes. I'm trapped down here with Lorne," he continued, his revelation causing Elizabeth's heart to sink a little more. Despite the fact that her two friends had been recovered at that moment, in that single heartbeat she would have given anything- even the knowledge that Rodney and Lorne were okay to know that John was okay instead.

"Are you guys okay?" Samantha yelled into the rock.

"We're fine," answered Rodney, followed a couple seconds later by, "Lorne's got a broken leg…"

"Alright McKay," Samantha called out. "Stay put we've got combat engineers here we're going to dig you out. "

"Well hurry up," the scientist replied sounding more worried than usual.

"We'll work as fast as is safe Rodney," she answered.

"No, no, No," he replied his voice sounding insistent despite being muffled. "You don't understand. I just found out when the self-destruct is initiated it's automatically programmed to send a sub-space burst. Michael's probably already on his way."

"It doesn't look like they're too far down," stated a young female soldier. "We should be able to get them out inside of an hour."

"Well what about the other two?" asked Jennifer with a quaver in her voice.

"They're a lot deeper," Sam answered with a sigh.

"They could be John and Ronan," stated Elizabeth looking at her newest friend with wide eyes. "We have to get to them Samantha…we need to know…"

Sam shook her head. "You need to know."

Elizabeth nodded weakly knowing that Jennifer was watching her. "Well the Daedalus will be here soon so we can just beam them out right?" asked the young doctor.

"As long as Michael doesn't get here first," Sam stated as she stood up and began to cal orders to the rescue crew. "Alright, lets get started….Rivers take a jumper into orbit and keep a lookout for Michael's ship I want to know the second he gets here."

-sparky-

Meanwhile, still deep under the rubble, Ronan was trying to get John free and John was berating himself for not seeing that the building would be booby trapped. Ronan for his part was trying to reassure John that the entire team knew what they were getting themselves into. That the all knew how dangerous it was going to be, it was a rescue mission after all. "You need to start thinking about how you're going to crawl yourself out of here…"

"Uh- no way."

"It's easy. You just keep moving up. Keep moving up and out of the debris. Work your way up," John stated.

"I'm not leaving you behind Sheppard," Ronan answered as he used their flashlight to search the area that they were in

"I'm not trying to be a hero here, it's a selfish thing," John stated as Ronan tried once more to move the beam of his leg. But it didn't work. "I need you," continued John. "To dig a hole, so that the rescuers can come down and get me…." John paused and ignored the fact that Ronan was digging down. "Someone has to let Elizabeth know that I'm still alive. She's probably going out of her mind with worry."

"We get this beam off you we get you free, we dig ourselves out together and you can tell her yourself. Deal?" asked Ronan as he continued to place concrete blocks on top of each other, not noticing that John was shaking his head.

"You aren't going to listen to me one way or another are you?" he asked.

"Great…deal," answered Ronan not answering at all.

-sparky-

Rodney pulled himself up and out of the hole in the ground with the assistance of the combat engineers. "Come over here," Jennifer muttered as she led Rodney to a semi-clear area in the rubble so that she could examine him- though Elizabeth was right behind them. She was waiting, and watching. A part of her was rejoicing that Rodney had survived, but another part was terrified that there was no way that her beloved could have survived as well.

"I'm fine it's just a couple scrapes."

"Wow, Rodney McKay refusing medical treatment. Now I know that something's wrong."

"Seriously, I'm okay. Just you should- look after Lorne."

Jennifer paused and turned to see Lorne. His face was a mask of pain and instantly she was at his side looking him over. That gave Elizabeth the chance to talk to Rodney, with Samantha right on her heels. "Rodney," Elizabeth muttered as she embraced her friend, not caring in the slightest that Rodney hugged her as tightly back. "You're alive."

Rodney smiled and laughed nervously. "I know. Amazing isn't it?"

"Any survivors?" asked Rodney watching as Elizabeth's face fell.

"You mean you don't know?" she asked her eyes widening. "You don't-"

"We found two life signs," answered Samantha as she came over to them. "But they were buried under a lot more debris than you were so it's going to take a lot more time to get them out. We've got people working on it."

"Good people," interjected Elizabeth with a forced hopeful tone in her voice. "They'll get John and Ronan out of there in no time."

"There's no guarantee that it's them," Sam stated honestly.

Elizabeth nodded and crossed her arms. "I know. But I have to believe that it's them. I have to believe that they're alive. I have to believe that we'll get to them before it's too late…"

"…so we don't know who they are?" asked Rodney watching the interaction between Elizabeth and Samantha carefully.

Sam shook her head. "Not yet," she stated honestly. "Listen Rodney, did you find Teyla?"

"No," Rodney answered with a sigh. "But I think Shepard was right. He was going to bring her here we were just early. We came too soon."

Elizabeth shook her head and gritted her teeth. "You think we would have figured out when she was brought here in the fifty-thousand years we had to wait for him…" she muttered darkly.

Rodney turned to Elizabeth. "Listen I don't think-"

"Go ahead," interrupted Sam as she spoke on the radio. She listened to the response and then turned to Elizabeth and Rodney. "Michael's here."

"Oh god," muttered Elizabeth as she leaned against a fallen column.

"We're out of time…." Rodney stated with equal horror.

"Everyone back to your jumpers," ordered Sam her voice carrying over the sound of the rescue attempt. The men and women who had been assigned to help get the survivors out of the wreckage began leaving the area when suddenly a young female soldier called out that they had darts in coming.

"Alright," Sam began after the first volley of fire was let loose. "Let's get back to our jumpers."

"We still have men trapped down there," stated Rodney.

"Sam we can't leave yet," Elizabeth agreed on her other side.

"They're going to have to wait," Sam stated. "We're no good to them out in the open like this."

Elizabeth shook her head. "I don't care," she stated her voice breaking. "I need to know. I can't leave…"

"Elizabeth,"

She shook her head. "Sam…please."

Sam shook her head. "Let's go, fall back."

And so they had no choice. They fell back to the jumpers. Into one ran Rodney, Elizabeth, Samantha and Jennifer. "Cloak the jumper," ordered Samantha as she took the co-pilots seat with Elizabeth behind her and Jennifer behind Rodney. Samantha then looked at the controls and her eyes widened. "We're getting a reading," she stated. "The gate's been activated."

Rodney sighed. "That's classic wraith battle technique. They dial the gate, lock everyone out and make sure that they can't escape."

Sam who was not that familiar with wraith techniques was impressed, though she did know that it was similar to what the goa'uld used to do back in the Milky Way galaxy. "Bastards…" she muttered looking at the controls.

"Yeah well they're not idiots," stated Rodney as he brought up the heads up display. "We've got more darts incoming and it looks like they have troops on the ground."

"They must know that we still have men alive down there," stated Elizabeth her voice bitter. "They must know that we left them behind."

"How many jumpers do we have?" asked Rodney completely ignoring Elizabeth's statement as he looked to Samantha.

"Three," Sam answered, including this one.

"I'm reading over twenty darts,"

"But they can't see us though," asked Jennifer. "Right?"

"Well not right now," answered Rodney. "But we can't fire while we're cloaked."

"Look, it's going to take them time to dig them out same as us," stated Sam. "We wait for the Daedalus. Rodney take us into orbit."

Rodney nodded and took the jumpers into the air and it was all Elizabeth could do from seizing the controls themselves and turn the jumper around. Upwards and upwards they climbed till they were in space. "There it is," muttered Rodney as the cruiser came into view.

"Is that Michael's cruiser?" asked Jennifer.

"Well it looks like it," answered Rodney with a great deal of irritation in his voice.

"Does that mean that Teyla's on that ship?" asked Jennifer again.

"Yes," Elizabeth snapped with irritation in her voice at the young doctor's naivety. "Yes that means that Teyla is probably on that ship. "

"Well that's great," stated Jennifer, ignoring the pain that was in Elizabeth's voice. "Right? When the Daedalus shows up we can just beam her up too no?"

"It's not as easy as that," corrected Rodney.

"Chances are Michael's already removed her transmitter," began Samantha.

"Even if he hasn't," Elizabeth continued. "Wraith cruisers are impervious to our beam technology. We can't get on and we can't get anyone off."

Jennifer couldn't believe it. "We're so close…" she muttered looking from Samantha to the cruiser in front of them. "…we can't be sitting right here and not do anything."

"We're not doing nothing," Rodney began as he looked behind himself.

"No," snapped Elizabeth. "Nothing is exactly what we're doing."

"Elizabeth," began Sam warningly.

"No," Elizabeth snapped again. "No. We're not doing anything to save the two men who are trapped down on that god forsaken planet and we're doing anything to save Teyla who good men risked their lives to try and rescue."

"Elizabeth," began Rodney.

"No," she interrupted. "No. I don't care what any of you say. We're doing nothing. I am sick of doing nothing and…" the emotion was too much. Elizabeth finally broke down and let some tears leak out of her eyes. Jennifer instantly reached out and hugged her friend as tight as she could. "…I can't lose him," she whispered as she buried her head into Jennifer's shoulder. "Not when we just got him back."

"I know," whispered Sam knowing what Elizabeth was going through, what pain she was in. "I know."

-sparky-

"Ronan, you need to get out of here."

"Would you leave me if I was stuck under there?" asked Ronan as he tried to get his breath back from trying to lift the beam once again.

"Yes," answered John coldly. "Even if you told me not to go…"

"Ah but would you leave if Elizabeth was stuck under there," asked Ronan again.

"Well of course not," John stated as his vision began to go in and out. "But that's different. She's my fiancée. I love her."

"Love comes in different forms Sheppard," Ronan stated gruffly as he looked his friend in the eyes. "It's a form of respect and a code of honour as well."

"What does that mean?" asked John, blinking his eyes.

"That means that I'm not going anywhere and…" Ronan began only to stop mid sentence as his ears picked something up. "…do you hear that?"

"What?" asked John, straining his ears to try and hear what Ronan was hearing.

"Sounds like digging," answered Ronan.

"Yeah, I hear it. I hear it." John muttered in disbelief.

-sparky-

The Daedalus arrived and raised their shields and Michael tried to run. Luckily Caldwell and his people got in a good shot and managed to stop them before they could initiate their hyperdrive.

"Daedalus," began Sam. "We still have two people on the planet."

"It is just a matter of time before the hybrids reach them," stated Rodney.

"Can you scan for transmitter signals?" asked Sam, hoping for Elizabeth's sake that the Daedalus would find John.

-sparky-

John and Ronan were screwed. They knew that those who were coming to rescue them were not their team mates, but hybrids. The few questions that they had asked them proved that much. "Bet he was tipped off when the building blew," stated Ronan as he made his way to sit next to John's head.

"Told yah that you should have gotten out of here," muttered John as he winced in pain. "You wouldn't be royally screwed now."

"Yeah whatever," mumbled Ronan as he reached for his gun.

John winced. "I can't reach my gun."

Ronan reached under the beam that had John pinned down and managed to grab the small handgun that was in its proper place. He loaded it and handed it to John. "Here," he whispered, his heart beginning to beat quickly with the adrenaline of the knowledge that a battle was imminent. "Alright," Ronan continued as he settled down once more. "How do you want to play this?"

There were a few poignant moments as John thought about what he was going to say, while struggling to think of a way to get out of the situation. When he realized that there was none, he stated the obvious. "Shoot till we can't shoot anymore."

Ronan looked up at the sounds of digging and nodded slightly. "Alright."

"Been a pleasure," John muttered as more dirt fell into their faces.

Ronan looked from the fallen ceiling to John and then back up again. "Same."

With no more left to be said they raised their arms and prepared to die. _I'm sorry Elizabeth,_ John thought to himself as his heart plummeted. _I'm not going to come back all in one piece…_


	23. Part II: Rescuing

**Chapter Two: Rescuing**

"We got 'em," stated Caldwell's left-hand man who was on radio to Sam's jumper as well. "It's Colonel Sheppard and Ronan." As soon as the words left his mouth the faces in the jumper widened with shock for none of them dared to believe the news. Rodney just looked to Sam who looked back to him. Jennifer caught a glimpse at Elizabeth who has broken down into tears of relief.

"Can you beam them up?' asked Sam, hoping for the best.

"We'll have to drop our shields," answered Caldwell over the radio. "I kinda think that that would be a bad idea right now."

"Look," snapped Elizabeth her voice holding all the authority that Caldwell had come to both respect and loathe over the past two years. "If Michael gets his hands on them, he'll kill them. We don't have a choice."

-sparky-

As soon as the jumpers were in the bay and as soon as Rodney let the hatch down Elizabeth was instantly out and running to the infirmary. She had to check for herself that John was alive. Despite the fact that they had told her that he was- she had to see it for herself. When she got there, Ronan was of course refusing treatment and John was being looked over by Keller. "We thought we lost you there," she was saying as she cleaned his wound.

"Yeah for a second there I thought that I had lost me," John muttered as he winced with pain. He looked towards the infirmary doors, away from Jennifer and saw the one person that he thought he would never get to see gain. "Lizabeth?" he breathed watching as her face crumpled with emotion.

"Oh John…" she choked out as she ran to his bedside and threw her arms around him, letting him do the same. "…John…."

"It's okay," John soothed. "Caldwell managed to get me out in one piece."

Elizabeth shook her head before burying it deeper into his neck. "Doesn't matter," she muttered. "I thought you were dead. You promised me once that you would stop making me believe that you were dead. Do you remember?"

That promise had been made just after he had come back from his suicide mission during the siege of Atlantis. "Of course I remember," he stated earnestly as he rubbed her back. "It's just that this is a dangerous business…."

"…speaking of," interrupted Jennifer as she continued to check out his wound. "You're going to be okay though you need some serious work. You should, you know, live to fight another day and all that."

Elizabeth sighed with relief. "Thank god."

"So," John began turning to Elizabeth. "What's going on? I take it that Michael showed up before the Daedalus."

Elizabeth nodded. "Yes. Steven had to lower the shields to get you and Ronan out of the debris."

John winced. "Tell him I'm sorry for that."

Elizabeth smiled and kissed John's sweat stained and bloodied forehead. "Well rest assured. With Rodney and Sam on the job I'm sure the ship will be ready for battle in no time."

"Rodney's alive?" asked John his eyed widening.

Jennifer nodded. "Yep. We found him and Lorne first."

"They were the only other two to make it out of the rubble," continued Elizabeth as she gripped John's hand tightly though she watched as he tried to sit up.

"Patch me up," John ordered. "I have to get back out there."

"No," Jennifer stated as she pushed him back down with her hand on one shoulder.

"Absolutely not," agreed Elizabeth as she held him down with her hand on the other shoulder. "John, you're injured."

"You will be fine," continued Jennifer "But you're far from it now. You've lost a lot of blood; you need surgery and a transfusion. I mean this- this can't wait."

"Look," John protested. 'Michael's here that means Teyla's probably on the ship. I'm to close, to sit here to do nothing."

Elizabeth shook her head. "You won't be doing nothing…"

"She's right," agreed Jennifer. "You won't be sitting and doing nothing. You'll be in surgery."

"Look," John began as he tried to sit up again. "Look there has to be a quick fix."

"No," stated Jennifer firmly.

"Something for a few hours."

"I'm sorry," Jennifer stated again. "I can't."

With that Jennifer turned to walk away but John grabbed her arm. "I have had the chance to rescue a team mate before and it slipped through my hands. I am not letting that happen again."

Jennifer sighed and pulled away, allowing Elizabeth to look at the man she loved. "Is this what this is about?" she asked looking at John with wide eyes. "You want to try and rescue Teyla. You want to make up for losing Ford."

John closed his eyes. "And you…"

"…I'm right here," she insisted. "John I'm right here."

"But I let you go," he shouted causing those in the infirmary to look at him though they quickly went back to their business. "I let you go," he repeated.

"Last time I checked I ordered you to let me go," Elizabeth stated as she placed a comforting hand on John's face. "And everything worked out in the end. I'm here aren't I?"

"But that doesn't change the fact that I let you go," John argued. "You. You're the most important person to me on this damn expedition and I was willing to let you go! When I thought that Kolya had killed you I wanted to make sure that none of those bastards got out of Atlantis alive despite the odds. And yet when you were right there in front of me I turned and walked away."

"John-"

"-what if Carter hadn't beamed you up?" asked John interrupting his fiancée completely. "What if you had been lost to us like Ford was."

"But I wasn't-"

"-but you could have been," John argued. "I could have lost you and I would have lost myself as well."

"You would have never given up hope," Elizabeth stated quietly. "You would have found me John. I know that and I knew that when I ordered you to go."

"I know that," he agreed. "But that doesn't change the fact that looking for you would have been like looking for a needle in a haystack just like it has been with Teyla. I- I'm not strong enough to say goodbye to anyone…" John muttered letting his emotions show for the first time in a very long time. "…and I've already had to say goodbye to far too many people."

"We could do nothing about Ford," Elizabeth assured. "John, he gave his life to make sure that you got out."

"Yeah but I was so sure that we would see him again."

"We still might."

John shook his head. "And Carson?"

"Carson was returned to us," Elizabeth pointed out. "Whether by the grace of god or not, the man that is in stasis is Carson Beckett. Clone or not I truly believe that," she paused and saw how he wasn't convinced. "We will find a way to cure him John. We will."

"And what about you?" he asked looking up. "You're going to live forever."

Elizabeth shook her head. "You don't know that."

"I do," he argued. "I've seen it."

"You saw a timeline where you were lost to us," she argued. "I may have been a full replicator there but I'm not now. The little buggers are keeping me alive, that's all."

"And what if they keep you alive forever?" asked John his voice breaking. "I don't want you to have to watch me die..."

Elizabeth shook her head. "John that is not going to happen; even if it does, it's life. People are taken away from us. Sometimes sooner than we would like but we move on- you moved on after your father's death same as I did."

"And if I died."

Elizabeth shook her head. "Honestly I don't know what I would do if I lost you," she admitted with a waver in her voice. "But I would make sure that I would live every moment from then onwards to its fullest. And losing you to old age is something that I will be able to handle," she paused and tried to block out the memory of when Kolya had John fed to the wraith. She had been sure that she was going to lose John to old age there, but she wasn't about to bring it up. "Just don't bail on me before then," she added.

"Elizabeth-"

"-John I know that you feel guilty," she interrupted. "I know that you want to go out there and rescue Teyla but you can't always be the rescuer."

"I have to," he stated quietly. "I don't know what else to be."

Elizabeth smiled and kissed him gently. "Just be John Sheppard. Just be the man that I love."

John sighed, took Elizabeth's face into his hands and kissed her back. "But the man that you love doesn't leave anyone behind, not if he can help it. Please," he stated pleadingly. "Let me go save her. Let me save her like I couldn't save Ford, or Carson, or you…"

"…you've saved me enough John," she stated quietly as she laid her head on his shoulder. "But I know that you have to do this," Elizabeth stated with a sigh as she looked into John's eyes. "You were born to be the hero John. You're my hero, you saved me so many times and now it's time for you to save Teyla."

John smiled. "Thank you for understanding."

Elizabeth smiled back and drew him into a hug. "Just come back to me in one piece John," she whispered. "Promise me that."

John held onto his fiancée as tight as he could. "I promise," he assured. "I swear."

-sparky-

"We could launch a 302 attack," suggested Samantha as she and Rodney did their best to repair the Daedalus before it was too late.

"That's what I was thinking," answered John as he, Ronan and Elizabeth walked towards the two scientists.

"Colonel?" began Samantha as she turned to face John. "Doctor Keller said that you were out of commission."

"She revised her diagnosis," stated John as he gingerly held his side which Elizabeth glanced at worriedly. She was not happy about letting John out of the infirmary, and neither was Jennifer but both women understood that this was who John was. He had to fight through the pain. He always had and he wasn't about to stop now. "Look," continued John as he glanced at Elizabeth and Ronan. "We might have an idea."

"There may be a way to get Teyla back," added Ronan.

"Really?" asked Rodney his eyes widening. "How?"

"It's not going to be easy," Elizabeth stated. "And we're going to need Steven's help."

-sparky-

"As a rule I like to keep daring rescues down to one a day," stated Caldwell as Ronan, Rodney, John and Samantha finished explaining their plan. "Though I don't have any other ideas…"

"As it stands shields are already down to twenty percent," began Samantha. "It's just a matter of time before they fail completely."

"I for one don't want to be around when that happens," interjected Elizabeth as she gripped John's arm. "And I don't want to let Teyla go. Not when we're this close."

"She's over there Steven," Samantha added. "Counting on us."

Elizabeth caught Samantha's eyes and finished her sentence. "We're not going to take no for an answer," she paused and caught Caldwell's eye. "You don't want to fight us on this."

Caldwell looked at the men and women before him. What they were proposing was crazy, but as he had learned since joining the Stargate Program- they were pretty much in the business of crazy and this plan could work. "Alright," he stated finally. "Take a cloaked jumper. Radio us when you're in position."

With that, one by one the team left the bridge. Elizabeth was the last to leave and she quickly caught up with her fiancée who was talking to Samantha. "John," Sam was saying as they walked through the corridors of the Daedalus. "What really happened in the infirmary?"

"Nothing," answered John still holding his side.

"So you're telling me if I go down there right now and talk to Jennifer she'll tell me that you're fit for active duty?" asked Samantha with a sceptical tone in her voice.

"I'm just trying to do my job," stated John as Elizabeth came to stand beside him.

"So am I," Samantha said earnestly. "And part of my job is determining whether or not you're going to be a liability on this mission."

"Colonel, I have more respect for you then any commanding officer I've ever had-"

"-hey-"

John flashed Elizabeth a smile. "You know what I mean," he stated before turning back to Samantha. "I'm getting on that jumper end of story."

"Don't worry Sam," Elizabeth assured as she held John's arm. "I'll be there to watch his back."

John looked to Elizabeth with surprise. "What?"

"Well you don't think that I'm going to let you have all the fun," stated Elizabeth with her usual grin. "I'm going with you."

John shook his head. "No way," he argued. "It's too dangerous."

Elizabeth glared at him. "I don't care. You're going because I managed to convince Jennifer how much this means to you. But I am not going to let you go all alone and risk getting killed. I'm going. End of story."

John sighed in resignation and nodded his head before turning back to Samantha who was shaking her head. "I am going Colonel," John stated. "I'll surrender for Court Martial when we're done."

And with that John walked away leaving Elizabeth and Sam standing in the hallway. "You better get going after him," Sam stated.

Elizabeth nodded. "Yeah," she paused and turned to the new commanding officer of Atlantis. "Listen, you're not really going to-"

Samantha shook her head. "No Elizabeth," she assured. "I'm not going to put John up for Court Martial. As far as I'm concerned aside from a few cuts and scrapes he's totally fit for duty. I'll make sure that that's what Jennifer puts in her report as well."

Elizabeth grinned and placed a friendly hand on Samantha's arm. "Thanks Sam," and with that she turned and left- following John's footsteps to where the jumpers were parked.

-sparky-

In the jumper there was John, Rodney, Ronan and Elizabeth and the later three people could see that their fearless leader was hurting something awful. Elizabeth saw out of the corner of her eye how Ronan and Rodney shared a glance, and in an instant she knew what they were going to say. "You know, Ronan and I could probably handle this."

Elizabeth crossed her arms in front of her chest. "And what am I Rodney?" she asked. "Chopped liver?"

"No, no. Of course not," stated Rodney. "It's just that I thought that if John wasn't on this mission then you'd-"

"Teyla's my friend too Rodney," Elizabeth interrupted. "I'm going. And so is John."

"Well then, maybe John should stay with the jumper," suggested Rodney, earning a disapproving look from both Elizabeth and John. "Or not," Rodney added quietly to himself as he turned his attention away from John.

John nodded and hit the communications button. "Daedalus," he stated his voice laced with pain. "We're in position."

-sparky-

The Daedalus launched the 302's, the dart bay opened and a swarm of darts poured forth. Unfortunately, the second that the last dart cleared the bay, something unexpected began to happen. "It's closing," pointed out Rodney with a touch of panic in his voice.

"I see that," answered John as he began to steer the cloaked and therefore invisible jumper towards the bay doors.

"It's closing quickly." Rodney pointed out again.

"I got it." John assured as he concentrated on flying through the searing pain that was emanating from the wound on his side.

"John-" began Elizabeth as she gripped the back of the pilot's chair.

"I said I've got it." John stated as the doors closed even further.

"John-" Elizabeth began again her sentence trailing off as John sped through the closing doors on an angle so that they could fit through the small opening. As soon as they were on the other side, everyone let out a sigh of relief. "Good job," she stated with a smile on her face as she gave John a peck on his cheek.

John smiled with appreciation at Elizabeth before radioing Caldwell and Sam. "Daedalus we're in," he stated and then without speaking he set the jumper down. John along with Ronan, Rodney and Elizabeth exited the jumper and began their search for Teyla.

They snuck through the ship, ignoring the hybrids yet keeping their guns poised to shoot at every second. John and Ronan were the most comfortable while Rodney was pouring over his technology and Elizabeth was trying her best to keep calm. She did not like going into these situations, but she wasn't about to let John out of her sight. Not for a moment. "Alright," state Rodney as he headed towards a panel. "This won't take more than a couple of seconds."

"Good," whispered Elizabeth. "Because I want to get out of here."

"Not without Teyla," added Ronan which earned a nod from John.

There was some beeping and Rodney got his 'concerned' face on. "That- troubling."

"What?" asked Ronan.

"Michael's more ahead with the repairs then I would have thought," answered Rodney. "The hyperdrive is almost back online."

"That's not good," muttered Elizabeth.

"No," agreed Rodney. "We're going to have to make this quick."

"How quick?" asked John.

"Well like, fifteen minutes," answered Rodney. "But that's not a lot of time."

"No," John agreed. "That's not a lot of time."

"Tell us where Teyla is," Elizabeth added. "We don't want to make any mistakes that will get us lost."

"Right. Right, right, right…" Rodney muttered as he went to work on his data pad. There was another beep and Rodney cracked a smile. "Got it," he stated as he double checked the location. "Follow me," he said as he began to lead them in the right direction. Ronan instantly took point with Rodney while Elizabeth and John took up the rear. Together, they were headed to save Teyla.

They rounded the last corner and instantly Ronan, John and Elizabeth all opened up fire on the hybrid that was standing guard. "John?" called out a voice from within the room.

"Yeah," John yelled back as they approached the door. "We're going to get you out of here."

"Just hang tight Teyla," Elizabeth assured as she too called out.

"Not a moment too soon," Teyla replied with laboured breath as she struggled to stand up. The door opened and John was the first one through. Elizabeth was next followed by Ronan and Rodney. Elizabeth instantly rushed to Teyla and embraced her, though as she did so two things happened.

Ronan was at her heals and stated; "We have to get you back to the jumper," though as he said that, Teyla fell to the ground and only Elizabeth and Ronan were able to hold her up.

"You okay?" asked John worriedly as he knelt down so that he could look in her eyes.

"It's my baby," answered Teyla.

"Is something wrong?" asked Elizabeth.

Teyla shook her head. "No." she replied. "I have been having contractions for over an hour now. They are very close. My baby is coming."

"Then we have to get you out of here," stated Ronan as he and Elizabeth helped her onto the crude examination table.

"I am sorry," Teyla apologized as she took a laboured breath. "I just need a moment." As the Athosian woman was saying that, Elizabeth noticed that John was still kneeling on the floor and that his wound had reopened.

"Good god John," she whispered as she knelt beside her fiancée. "I knew that this would happen."

John shook his head and gritted through the pain. "I'd carry her buddy," he began as Elizabeth helped him to his feet. "But I'm not really up to it."

"Damn straight your not," muttered Elizabeth angrily. "You shouldn't be here."

"I have to be here," he argued back. "And you know it."

Ronan looked at the arguing couple and then looked back to Teyla. "Alright," he stated as he moved towards her. "You ready?"

"I can walk," Teyla assured as Ronan inched back away from her. "I just need a moment,"

"Uh say friends," stated Rodney bringing all attention back to the problem at hand. "We have a small issue here."

"Ugh," moaned John. "What now?"  
"Looks like Michael has got his hyperdrive back online."

"It's powering up?" asked Elizabeth watching as Rodney nodded.

"Can you shut it down?" asked John.

"Not from this little thing," Rodney replied. "Look the hyperdrive room is just down the corridor. You slap a C4 charge on that thing and it should certainly be shut down."

"Where?" asked Elizabeth taking charge of the situation as she saw John wincing in pain.

"Here," Rodney stated. "I've got a map."

Rodney then held out the data pad which Elizabeth took first, followed by John. "Alright," John stated. "Ronan- you're with me."

"So am I," Elizabeth stated earning a resigned nod from John.

"I'll be right back," Ronan assured as he stood up and for the first time Elizabeth saw the emotion behind his eyes. "Everything is going to be fine," he continued as he took Teyla's hand. Together, John and Elizabeth led the way with Ronan pausing only briefly to have some words with Rodney.

-sparky-

Ronan took point and instantly shot the guards who were watching the hyperdrive engine. There were three of them and before any of them could react they were all dead. Ronan, John and Elizabeth took one moment to look at the immense cavernous room. "It's almost powered up." Ronan stated breaking the silence.

Elizabeth nodded and held out her hands. "Give me your C4," she stated and without arguing both John and Ronan handed the small cartridges to her. Wasting no time, despite the fact that John collapsed against a panel, Elizabeth made her way to the underside of the hyperdrive engine and placed all three of them in a triangular pattern. "Alright," she stated as she took a step back. "Ready."

"Let's go," Ronan stated taking point with Elizabeth supporting John the best that she could behind him. On their way back to where Teyla and Rodney were waiting they encountered some resistance which Ronan made quick work of.

"Alright," John stated as they hid around one of the corner. "Let's hope we're far enough away."

"Yeah," agreed Ronan as John pulled out the trigger. "Lets see."

John took a deep breath before looking at Elizabeth who was standing in between the two men. "Fire in the hole," John muttered as he flipped the switch. The explosion was loud and resounding and it shook the ship.

"That's going to grab Michael's attention," Ronan muttered.

"We're going to get out of here," Elizabeth stated. "Fast."

And with that, they continued on their way to where they had left Rodney and Teyla. Running as quick as they could and as fast as John's battered body would allow they entered the room where they had left Rodney and Teyla. Only there was something different. "Oh Telya," Elizabeth cooed as she raced to her friends side. "He's beautiful."

"Wow," muttered John as he stepped up behind Elizabeth.

Rodney looked quite pleased and quite amazed with himself. "Yeah," he agreed. "I caught it. It didn't hit the floor or anything,"

Teyla smiled bigger, though Elizabeth didn't think that ti was possible. "He was amazing," she stated, breathless herself.

"That's good," John stated. "Good job Rodney."

"We have to get you out of here," Elizabeth stated.

Teyla nodded. "Ronan," she began. "You're going to have to help me." She held her baby son tight as Ronan picked her up effortlessly. Together the five of them made their way back to the dart bay- but the jumper was no longer there. It had been moved or stolen. "Told you, you should have stayed here,"

John shook his head and he led his team away from the bay. Trying to find a way out they encountered Kanann and he helped them to escape by using a dart which John piloted.

-sparky-

Back in Atlantis, with Micheal's ship destroyed and hopefully Michael along with it the team was doing what they needed to do. Teyla was resting comfortably in the infirmary with her son and John was getting prepped for surgery. Rodney and Elizabeth were making their way to the infirmary when they ran into Sam. "They found the last Ba'al clone," she stated. "They're going to extract the symbiote and they want SG1 to make an appearance."

"Sounds fun," stated Rodney.

"Plus," Sam continued. "The IOA wants to do an exhaustive review of my first year in command. So you know- that can't be good."

Elizabeth smiled sympathetically. "Oh don't worry. I'm sure that you'll be back to us in no time."

Sam nodded. "I suppose, but I'm sure that you want your office back right?"

Elizabeth nodded. "I would be lying if I said that I didn't. But you've done a good job this past year. You should be very proud."

"Yeah," Rodney agreed. "They probably want to give you a medal, you had a great year. I know my opinion doesn't mean much to those folks but-um- I think you've done an excellent job. I'm glad you took the post."

Elizabeth poked Rodney in the arm. "Oh and I was so terrible?"

"What?" asked Rodney his eyes widening. "No, it's just that circumstances being what they were…."

Elizabeth smiled. "Don't worry 'bout it Rodney."

"What?" he asked in confusion, though he got it. "Okay."

"Thanks Rodney," Sam interrupted. "That means a lot."

"Uh Sam?" asked Elizabeth. "About the Court Martial?"

Sam smiled. "It'll have to wait."

"Can't you just forget about it?" she asked hopefully.

Sam nodded. "Sure."

"See you soon," Rodney stated as Sam turned to leave.

"Have fun," Elizabeth stated as she too followed Rodney.

-sparky-

Elizabeth and Rodney walked into the infirmary to see John and Teyla talking. "I'll be off my feet for a week or so," John was saying as he worked on his small data pad.

"I can't believe you attempted a rescue mission in your condition," Teyla stated unbelievingly.

"You're telling me," Elizabeth agreed as she walked into the infirmary.

"Hey," John protested. "Last time I checked, I succeeded."

Teyla nodded and Elizabeth made her way to John's side. "How's the baby?" she asked as she sat down on the edge of John's bed.

"Well Doctor Keller says that he's perfectly healthy," Teyla began as she looked lovingly at her son with Rodney looking down on the boy as well. "I'd say that he's perfectly everything."

John smiled and took Elizabeth's hand. "That's great."

"Really, really great," Rodney agreed.

"I want to thank you," Teyla stated. "Both of you…all of you."

"There's no need," John replied.

"No need at all," Elizabeth agreed.

"I never gave up hope," Teyla continued. "Because I knew, I knew that my family would come for me."

John looked away sheepishly. "You would have done the same for me," he stated. "Or any of us."

"Yes," Teyla assured. "I would have."

"Alright," interrupted Jennifer as she came into the room. "You ready Colonel?"

Elizabeth nodded. "I think he's ready."

"Ready?" asked John being cheeky. "What do I have to be ready for? From what I understand I won't be doing anything."

"Well that's right," Jennifer agreed. "You just have to stay still and let me fix up your innards."

"So long as you put them back where they're supposed to be," Elizabeth stated, enjoying the joke at John's expense. There was a couple seconds of awkward silence which Elizabeth broke by giving John a kiss on the cheek. "Sleep tight John," she whispered.

"Let's go," Jennifer stated, calling over her assistants.

"What are you going to name the baby?" John asked out of curiosity as he was wheeled out of the infirmary.

"Well, if it's alright with the both of you I was thinking of Torren John." Teyla stated. "After my father, and after you."

Elizabeth smiled. "I think that that is a wonderful idea."

"Me too," John agreed. "I'd be honoured."

"What?" asked Rodney his eyes widening.

"McKay hates that," Jennifer pointed out, earning a grin from Teyla.

"I did deliver the kid," Rodney protested. "But it is of course Teyla's choice…But what about Kenann? Will he mind?"

Teyla sighed. "Until you are able to bring him back to himself he will have to make due with the decisions that I make."

Jennifer sighed. "We're doing our best. But Carson's research is a little spotty."

"I know," Teyla stated. "I know and I can be patient. Torren John Emmagen and I shall be fine."

"We'll take care of you," Elizabeth assured as she kissed John goodbye. "You'll have nothing to worry about." She watched as Teyla nodded. None of them would have much to worry about, so long as they faced the future together.

_AN- There you go. It's going to be a couple of weeks before the next chapter is out. Sorry gang. Please take the time to read and review and what do you all think about the title **Tides of Atlantis**_**?** _Do you like it? Does it suit this story? Please lemme know and I'll see you guys in a couple of weeks once Season 5 of Atlantis actually does air. _

_Ta!_


	24. Part II: Back to the Roots

_A/N- I know that I'm a week behind but the essay for my summer class and issues with my old job have been taking up the majority of my time. Sorry._

**Chapter Three: Back to the Roots**

An hour after Samantha had left Atlantis, Elizabeth was called to the gateroom. There was an incoming wormhole and the person on the other hand wanted to talk to her. "Samantha?" asked Elizabeth as she regarded the woman on the screen. "What's up?"

"Elizabeth you need to gather your things and dial back to Earth within the hour."

"What?" asked Elizabeth not understanding what Sam was asking of her.

"Elizabeth," Sam stated again. "Trust me. You have to come though the gate."

"But John-"

Sam shook her head. "I know John's in surgery, but you have to come now." She fell silent and watched Elizabeth's face. "Please, I'll explain everything once you're on this side, but you have to come now."

Elizabeth nodded stoically. "Alright. I'll see you in the hour."

—sparky—

Three weeks later, John and Rodney were in the control room awaiting the arrival of their new commander. Rodney was on edge, but John was operating with a barely controlled sense of panic. It had been three weeks since he had last seen or heard from Elizabeth, his fiancée and he was hoping that whoever the new commander was that he or she would be able to tell him what had happened. _This isn't fair,_ Rodney had remarked once they had learned that Sam was being replaced. _I mean who's this new guy going to be._

_Rodney's right,_ Jennifer had agreed one night when the senior staff had met to discuss things. _I mean, if anyone is going to replace Sam it should be Elizabeth._

_That's right,_ John himself had agreed. _Why can't Elizabeth get the post back?_

_You have not heard from her,_ Teyla had asked quietly. _Have you?_

John had shook his head. _No._ he had told them_. Nothing yet…_

_Hey buddy,_ Ronan had stated. _I'm sure you'll hear something soon._

Three weeks later, nothing had been heard.

"Sir," began on of the new technicians who was training next to Chuck. "Sir the Daedalus just dropped out of hyperspace."

"We're receiving a signal," Chuck continued. "Colonel Caldwell is requesting that the new commander of Atlantis be beamed down."

Half-heartedly, John nodded and stood. The rest of the technicians followed suit and Rodney finally dragged himself to his feet. Then in a flash of light an Asgard transporter beam blinded all for a moment, but when the light cleared, they saw who their new commander was. "Elizabeth?" John asked, his eyes wide as he took in her longer hair which was pulled back into a pony-tail and the red command uniform that she wore. "Is it you?"

Elizabeth smiled widely and nodded. "Yes. The IOA have decided that with my expert knowledge and the decreased military threat, that I could be reinstated as the commander of Atlantis."

"Well that's—that's great!" Rodney stated, stumbling over his words in shock. "Welcome back."

Elizabeth nodded in her usual leaderish manner and John could feel a knot growing in the centre of his stomach. "Chuck," she began as she put on her radio earpiece. "Put me on city wide."

"Yes ma'am."

"Atlantis," Elizabeth began her voice echoing throughout every corridor and room in Atlantis. "This is Dr. Elizabeth Weir. I'm sure many of you have been wondering about what I've been doing on Earth these past three weeks but the truth is I wasn't there for more than a few hours. After being briefed by the representatives of the IOA, I boarded the Daedalus and I return now as the commander of the Atlantis Expedition." Elizabeth paused for a moment and smiled to herself. "I know that it has been a very long year for all of us but I want you to know how proud I am of each and every one of you. Together, we've managed to destroy the replicators and the wraith are in disarray. We will still have to be on our toes however, the Pegasus galaxy is a big place and I want us all to be safe and sound in our exploration of it. I look forward to working with each and everyone of you once more, and I promise that I will be the same Elizabeth Weir that you all grew to know in the first three years here. That is all…" she paused and nodded to Chuck who took her off city wide.

"Now," Elizabeth continued as she turned to face John and Rodney again. "I'm going to go into my office to settle down and I would like to have a briefing with the senior staff first thing in the morning. I've been out of touch for three weeks and I would like to be caught up as soon as possible…" she paused again and smiled as she turned to Chuck and the new technicians. "Chuck, I have a couple of boxes aboard the Daedalus, could you have them sent to my quarters?"

_Our Quarters,_ thought John silently, but he said nothing as Chuck nodded. Elizabeth smiled widely at all of them and then took herself off to her office. John, not paying attention to Rodney's elated ramblings followed her and closed the sliding glass door behind her. "Elizabeth," he stated with more emotion in his voice than he would have liked. "Do we-"

"John?" she asked, not knowing what he was trying to say.

"Are we going to have to have a talk?"

Elizabeth looked at him blankly. "What do you mean?"

"I mean that you're in command again," he explained as he sat on the edge of her desk like he had done so long ago. "What does that mean for us?"

"What about us?" Elizabeth asked, a smile still on her face.

"Are you going to shut me out?" he asked bluntly. "You told me once that you didn't pursue a relationship with that scientist because you didn't want your focus to be split and—"

"Oh John," she interjected as she stood up to come face to face with her fiancée. "Is that what you're worried about?"

Numbly, John nodded.

"Oh John," Elizabeth stated as she put her arms around him. "Nothing between us is going to chance, I swear."

"But the IOA—"

"They have no say what I do in my private life here," she interrupted as she pulled back and looked him right in the eyes. "They know that while I sometimes let my emotions rule my decisions, even when my dearest friends are in trouble I will put the needs of the city first…" she paused and thought back to their third year in the city. "…do you remember when Kolya had captured you?" she asked quietly. "He wanted a trade and I wouldn't do it…"

"I told you not to,"

Elizabeth shook her head. "I know that, but I could have. I would have…my feelings for you were the same then as they are now and…" she paused and looked at John in the eyes. "…and it's going to be difficult and I'm always going to be a nervous wreck when you go through the gate now but that's not a new feeling for me."

"So losing your friend is different then losing your fiancée?" asked John.

Again, Elizabeth shook her head. "No it's exactly the same…and losing my fiancée…" she paused and tried to brighten up. "Well, I just need you to promise me that you'll be careful out there…can you do that?"

Gleefully, John nodded. "Of course, I have a fiancée to come to now."

Elizabeth smiled and kissed him, and John kissed her back.

—sparky—

"It's not just that," Rodney stated as the senior staff gathered, Elizabeth no where to be seen yet. "I mean, Sam didn't exactly stick to protocol."

"Neither did I," Elizabeth stated as she entered the briefing room. "But don't tell me Rodney that you're not happy to see me back?"

"What?" asked Rodney stuttering, "I uh-"

"Relax Rodney," Elizabeth interrupted with a smile. "What ever the reason, the IOA wanted someone that they could trust in command, and I guess they felt like they could trust me."

"Well, I'm just glad that the future events aren't going the way Colonel Sheppard foresaw when he was catapulted into the future." Jennifer stated with a sigh of relief. "I mean, that must mean that future is what you make it. Woolsey isn't in charge of Atlantis, and Michael's not running the galaxy—"

John nodded gratefully. "Yep, the future's a whole new can of worms now."

Elizabeth smiled. "Speaking of the future, do we have any idea where Michael might be? His organization has been dismantled and—"

"And we haven't found him yet." Ronan interrupted.

"Well we're not going to stop trying," Elizabeth assured. "Though it's not going to be you guys," she paused and saw the protests coming but she shook her head. "I know that you all want revenge on him, but it's not going to be possible. Lorne's team will be heading up the search and you guys will return to your normal activities."

"Exploring," John stated.

Elizabeth nodded. "Right…now, for the Athosian-Hybrids they're still on the mainland?"

This time it was John who nodded. "That's right."

Elizabeth smiled. "And how is their rehabilitation progressing?" Elizabeth paused and looked at Jennifer who was lost in thought. "Jennifer?" she asked.

"Um, right." Jennifer began as she was startled back into the conversations. "Uh well um, we've had some success using a slightly modified version of the original retrovirus that created Michael in the first place. It weeds out the Wraith D.N.A. and allows them to resume their original human form over time."

"Without any last lasting ill effects?" Elizabeth asked.

Jennifer shook her head. "None that we've detected so far no."

"Many have already completed the treatment," Teyla interjected. "They're wondering when they might be released…"

"I see no reason for those who have completed the treatment to return to New Athos," Elizabeth stated with a smile.

"Actually," Teyla stated. "Kenann and some of the others would like to stay here in the city for the time being until my people accept them again." She paused and took a deep breath. "I know that I am asking a lot, but those who were violated against their will do not feel as though they are ready to return to the lives that they once lived and—"

"And think nothing of it." Elizabeth assured with a sympathetic smile. "Kenann and the other can stay in Atlantis for as long as they would like…" she paused and smiled again. "Besides, I'm that the father of your baby would love to be near your son."

Teyla nodded and smiled widely. "We both would like that."

"Now," Elizabeth continued as she flipped to another note. "Jennifer you've been giving Carson a lot of attention in the past three weeks. Have you found anything?"

"Maybe," Jennifer stated. "We found a serum that -- in lab tests at least -- seems to be capable of stabilising the clone cells."

"Can he be revived?" Elizabeth asked.

"Carson was near death when we put him in that chamber. I don't wanna take him out until I know for sure. But lab tests can only do so much."

Elizabeth smiled and held out a control crystal for Jennifer. "Try this on for size," she stated warmly "It's a gift from Doctor Jackson. He managed to find the Asgard research on the Jack clone who's now a musician from what I gather…apparently if you use what's on there, even if the serum doesn't work this will."

—sparky—

They waited and waited and finally, Carson opened his eyes. "Hey there," Elizabeth stated warmly as he glanced at them. "How are you feeling?"

"Fine," Carson answered. "What happened?"

"What do you think happened?" Rodney asked. "We thawed you out."

Teyla smiled. "It is nice to see you again Carson."

"Yeah," Ronan agreed. "What's up Doc? It's been a while,"

"Aye," Carson replied softly. "How long was I in there?"

"Two months," John answered. "Give or take."

"Did I miss anything?"

John smiled. "Well if you mean dismantling Michael's operation and helping the hybrids to return to their original selves anything then yeah…it's been a busy two months."

Carson smiled as Jennifer walked int. "I've got good news for you Doctor Beckett," she stated softly. "At the moment you're showing no signs of cellular degradation."

"You were able to recreate the treatment?" he asked.

Smiling proudly, Jennifer nodded. "That's right," she stated somewhat awkwardly. "I'll let them tell you about it."

"Hey now," Elizabeth stated. "Stay here. You've done a good job Jennifer."

"Aye," Carson agreed, catching Jennifer's eyes. "You have luv. Thank you. I owe you one."

Little did Carson know that a mere day later, he would have to jump back into things.

—sparky—

"Oh my god," Carson muttered as he entered Jennifer's isolation room in a hazmat suit. "Jennifer."

"Carson?" she asked frightened. "What's happening to me?"

"We're, we're not entirely sure," Carson stated honestly. "It looks like some kind of cocoon. Are you in pain Jennifer?"

"No," she answered, clearly frightened. "I can't feel anything…I can't move."

"Oh luv," Carson sighed as he stepped up as close to her as he could and placed a comforting hand upon her head. "Don't you worry now, alright? We're going to get you out."

—sparky—

"How are things?" Elizabeth asked later, once Carson had finished his visit with Jennifer.

"Not well," he stated honestly. "She's claiming that she's hearing voices, and the rest of the team have traces of this organism in their blood."

"But not me?" Elizabeth asked again.

Carson shook his head. "No luv," he stated. "Not you."

"And the thing?" asked Elizabeth once more.

"It doubling its mass every couple of hours, pretty soon it could be a real threat to the base."

Elizabeth sighed. "Keep me apprised."

—sparky—

In their quarters, John was pacing frantically as Elizabeth explained the situation to him. "Right now, we're working under the assumption that this alien pathogen was present somewhere in that lab, possibly as part of one of Michael's experiments. When the building was destroyed, it was released."

"We've been back for almost a month now," John stated angrily. "If it was going to spread to the general population don't you think that it would have already happened?"

Elizabeth sighed. "I know, and Carson is confident that it's not contagious."

"Then why confine us?'

"You've seen what's happening to Jennifer," Elizabeth pointed out.

"Yeah," John agreed angrily. "But it's not happening to me."

"But it could," Elizabeth shot back, just as fiercely. "You have it in your blood John. There could be any number of random physiological reasons why it started with Jennifer but that's no guarantee that it's not going to happen to the rest of you. It could be a matter of days; it could be a matter of hours. Even Sam's been quarantined back at Stargate Command and I've already been screened and I'm clean" she paused and softened her voice. "Look, I know it's hard for you to stay on the sidelines, John but it's the right call."

John turned his back to her, and Elizabeth took that as her cue to leave. Just as she was at the door he turned and spoke to her. "In the meantime, what are we gonna do about Keller?"

Elizabeth paused and turned back to her fiancée. "At the moment I'm not sure," she stated honestly. "But I swear to you John, I'm not going to let her go without a fight, and neither will Carson." And with that, Elizabeth left John alone, knowing full well that there was nothing that she could do for him at the moment.

—sparky—


	25. Part II: Root of the Problem

**Chapter Four: Root of the Problems**

"Dr. Weir," began Radek as Elizabeth walked into the control room. "We have a problem."

"I know that Radek," she stated with a nod.

"No I mean we have another problem," he insisted, motioning for her to join himself, Carson and Teyla by one of the various screens in the control room.

"There," Teyla stated as she pointed to the screen. "One of the city's main power conduits runs beneath the building that Jennifer is in right not."

"Alright," Elizabeth said. "Then we shut down the power in that section too."

"No, No." Radeck protested. "We already did. This conduit runs directly into the ZeeP.M. It's like an express lane. Uh, we've already shut off the rest of traffic but this one keeps moving along."

"The only way to stop it would be to pull the ZPM and shut off power to the entire city." Teyla answered.

Elizabeth looked from Radek to Teyla and sighed. "Why do I get the feeling that this is the plan of one Doctor Rodney McKay…"

Teyla sighed. "I did talk to him and while I understand that this thing has an effect on their minds—"

"Rodney isn't wrong about this," Radek interrupted. "If it reaches the conduit, it will have access to virtually unlimited power."

Elizabeth closed her eyes feeling a migraine coming on. "And what would happen?" she asked although she already knew the answer.

"The growth would increase exponentially." Carson answered.

"And since we've shut this section down," Radek continued "—we have no sensors in the area, so the only way to know how far it's penetrated is to do a visual inspection."

Elizabeth sighed and nodded. "Okay, assemble a team."

Radek and Teyla instantly took their leave and Elizabeth turned to Carson. "I need some answers," she stated quietly. "We need to kill this thing. Do you have anything?"

"We're working on a genetically engineered virus that might be capable of destroying the pathogen that's infecting Doctor Keller, but that wouldn't eliminate the biopolymer itself." Carson explained.

"What would?" Elizabeth asked.

"At this time luv," Carson answered sadly. "I have no idea."

—sparky—

Carson finally came up with a suggestion, which Elizabeth knew that she would have to take to John, Rodney and Ronan. "We turned the power back on briefly to get a look inside the building John," she explained as she handed a computer tablet to him. "This is the ground floor, five floors _below_ the Isolation Room," she paused and let the three guys look at the image. It depicted the walls and floors covered with the tendrils. "As you can see, access is almost completely choked off, but for this to work, I need someone to step right up to Jennifer's bed and inject her."

"Well, we can use the transporter to get them close, but ..."

"But someone would still have to run a gauntlet of over fifty metres Rodney," Elizabeth interrupted. "And after what happened to Radek I need something else. Something that won't risk anymore lives."

"So test the drug," Ronan suggested. "I've got the same thing in me, I'll take a shot right now."

"S-so, so will I," Rodney agreed, though his stuttering betrayed the fact that he was less than enthusiastic about the prospect.

"No. No, no." John stated looking to both Rodney and Ronan before staring Elizabeth in the eyes. "I'll do it."

Elizabeth took a deep breath and tried to keep a straight face. "John-"

"As the military leader of this expedition I have a right to ensure that none of my people are put in any undue harm."

_And what about your fiancée to be?_ She thought to herself, but as soon as the thought had crossed her mind she knew that John would never accept her arguing with him and therefore, she agreed. "Alright then," Elizabeth stated in a quiet voice. "Let's get you down to the infirmary."

—sparky—

"Restraints, huh?" John asked as he was tied down to the infirmary bed.

"Aye," Carson confirmed. "I'm sorry, but I'm anticipating a severe reaction."

"Oh great," John stated with a sigh.

"John," Elizabeth began one more time. "Are you one-hundred percent sure that you want to do this?"

John said nothing but nodded and Elizabeth showed her support by giving him a kiss on his temple. "Alright then love," she whispered. "This is your call."

"Now you must understand," Carson explained. "This formula comes from Michael, so as far as we know, it could ..."

"... turn me into a bug?" John interrupted as Elizabeth grabbed his hand supportively. Neither of them wanted to be put in that situation again. It had taken weeks for the two of them to move past what had transpired and while they were both certain that they would be able to deal with any unexpected side effects, neither Elizabeth nor John wanted to be put in a seemingly hopeless situation again. "Been there, done that."

"No actually, I was going to say it could kill you." Carson finished.

Elizabeth gripped John's hand tighter and he just nodded. "Just give me the shot."

"Okay," Carson stated as he injected John in the neck. Now, it should take a few minutes to kick in, so just try to relax."

"Oh, Okay," John replied sarcastically. "I'll, I'll just, I'll relax."

"I love you," Elizabeth whispered as she heard Rodney asking if some of the others were beginning to show symptoms, which they were. "I'll love you no matter what," she continued. "You know that don't you?"

John nodded and took Elizabeth's hand the best he could. "And I love you Elizabeth and you know that I wouldn't be doing this if—" Just then, John grimaced and started to convulse gently.

"John?" Elizabeth asked worriedly before turning away. "Carson!"

Carson, Rodney, Ronan and Teyla hurried over. "Oh," John stated through gritted teeth. "I think the restraints were a good idea." John started to convulse more strongly and they all watched as he began to writhe in agony. The shot was working.

—sparky—

Elizabeth would have loved to have stayed with John throughout the entire ordeal; however she was not just a member of the expedition anymore. She was the leader again and as such she could not be supporting her fiancée in person but by supporting him from afar in the control room. "What's our status?" she asked as she entered the hub of the city.

"Well, the Infirmary and a few other essential systems have been switched to emergency generators." Radek answered nervously. "We're ready."

"Alright," Elizabeth stated with a sigh. "Pull the plug,"

Radek typed onto the appropriate keyboard and the entire city went dark. Elizabeth turned on her flashlight and immediately made a bee-line for the infirmary again where John was still convulsing with Ronan holding him down. "For God's sake, Carson," she stated as she came to stand beside her fiancée. "How long is this gonna go on for?"

"I'm sorry luv," Carson answered. "I have no idea."

"Hang on John," Elizabeth stated as she leaned close to her love. "I'm here."

But Elizabeth being there did nothing for John. His heart rate increased dramatically in the span of a couple seconds and then as the monitor's flatlined, John stopped moving. "Oh god," Elizabeth muttered as her breath hitched in her throat. "Carson!" she cried out, Carson ran over to her and pushed past her to check John's pulse.

"His heart has stopped," Carson stated as Elizabeth stepped back to give her former CMO some room. "Bag him!" he ordered. "Get a crash cart in here! Prepare to intubate!" One of the nurses, whose name escaped Elizabeth's memory at the present time began to pump air into John's lungs while Carson began the basic CPR on his chest. "One, two, three. One, two, three. One, two, three. Come on. One, two, three. One, two, three."

"Come on John," Elizabeth pleaded from the sidelines, her hands clasped in front of her face. "Do not leave me like this…" Finally, the heart monitor began to stutter and then displayed a very slow pulse. Carson instantly checked John's neck and the nurse took the air pump away. "Is he—"

"He's back," Carson confirmed as John took a breath on his own and opened his eyes. He turned his head to the side weakly. "He's back."

"How'd I do?" asked John weakly.

Elizabeth let out a relieved laugh and kissed his forehead. "You did great."

—sparky—

"So it worked right?" asked Elizabeth moments later as John was talking to the rest of his team. "I mean, there's no lingering ill effects?"

Carson shook his head. "The blood screen came up negative," he stated. "So as far as I can tell luv, the alien pathogen has been eliminated."

Elizabeth sighed with relief. "Well done," she stated with an honest smile as she reached over and hugged the friend that she had missed for so long. "It is good to have you back."

"Aye luv," Carson agreed, hugging Elizabeth back. "It is good to be back."

—sparky—

"Alright," Elizabeth began as she spoke to Rodney, Ronan, Teyla and Carson minutes later. "We need a volunteer—"

"I'll do it," Rodney offered reluctantly.

"I'll do it," Ronan offered more earnestly.

"I'll do it," Carson offered almost desperately.

Elizabeth took a deep breath and looked at the three of them. Rodney was only offering because he felt as though he owed Jennifer something, Ronan was offering because if Elizabeth was reading the signs right he was beginning to care for the young doctor and Carson was offering to administer the drug for a reason that Elizabeth could not discern. She assumed that it was because Jennifer had inturn saved his life, but there was something else behind Carson's eyes, something more than a need to complete a debt. But who to chose? She didn't know, but she had to consider who would be able to complete the mission. "Carson," she began slowly. "No special medical skill is required to administer the drug right?"

Slightly frustrated Carson nodded. "That's right."

"Alright then," Elizabeth continued. "While I understand your willingness to help save Jennifer, I have to look at this logically. Ronan I think that you'd have a better chance of making it through the clogged hallways because not only are you the most agile of the three of you but I assume that this is like the same situation with John when he was turning into a bug."

"Aye lass,"

"Then Ronan," Elizabeth stated. "You have a go."

—sparky—

"Alright," Ronan called over the radio. "I'm in."

"Very good Ronan," Elizabeth answered. "How does it look?"

Ronan shook his head even though he knew no one could see him. "Not good."

For the next several moments he was silent, but they could hear his breathing as it increased. Slowly, Ronan made his way forward. "What's your status?" Elizabeth asked about ten minutes later. "Are you any closer?"

"It's getting harder to move," Ronan answered. "There's just too much of it."

"Remember the situation with John," Elizabeth stated. "Be unthreatening."

"Uh that might be a problem," Ronan said back.

"And why is that?" asked Elizabeth.

"I can't go any further," he answered. "The corridor's completely blocked. All right, so what d'you want me to do?"

John came into the control room at that moment. "Don't do anything," he stated over the radio, nodding to Elizabeth to let her know that everything was alright. "Just stay calm and stay there, I have a plan." He turned to Elizabeth then and knowing that there was no time she nodded in support. "Ronan," John continued as he ran up the stairs towards the jumper bay. "I'm going to take a jumper and get within a corridor or two from the isolation room. Stay where you are and don't blow anything up, that's an order." He paused halfway up the steps and turned around. "Elizabeth, open a channel to Doctor Keller, get her talking if you can"

Elizabeth nodded in understanding and before she could say anything else, John was gone. "Open a channel," she ordered and nervously Radek nodded. "Doctor Keller?" she asked. "Jennifer, this is Elizabeth can you hear me?"

"I hear you," a different voice said "—but I'm not Doctor Keller any more."

"Then who are you?" asked Elizabeth, wondering how John was doing.

"I have no designation yet. I'll be given one when I'm complete."

"So it is a ship," Rodney whispered. "We were right."

"What about Jennifer?" Elizabeth asked again.

"There is no Jennifer, only me."

"Jennifer," stated Carson as he activated his headset. "This is Carson,"

"Doctor Beckett, I already told you. I am not Jennifer Keller any more."

"You're the voice she was hearing -- the part of her mind that was taken over." Carson stated, knowing that he had to keep Jennifer, or whatever had taken over her mind talking until John could complete the plan, whatever that was.

"You can't stop me. I will become as I was meant to be."

Suddenly a rumble could be heard and Elizabeth instantly ordered for a secure radio channel to John. "John?" she asked. "John can you hear me?"

"Seems as though the Colonel rammed the jumper into the building," answered Chuck. "It and the building seem to be fine though."

"John? Elizabeth asked again, her voice holding a note of panic in it. "John?"

"I'm here," came a quiet voice. "That hurt more than I thought."

"Be careful John," Elizabeth ordered. "Don't do anything stupid."

—sparky—

"How's Ronan?" asked John once everything was over.

Elizabeth sighed. "He has a bruised larynx. Apparently he won't be able to speak for several days…" she paused and raised an eyebrow at John. "Wonder if anyone will notice the difference."

"Colonel Sheppard," Carson stated as he walked over with Jennifer at his side. "Look who's finally out of isolation."

"Good to see you up and about Jennifer," Elizabeth stated warmly.

"How are you feeling?" Jennifer asked concernedly.

"It only hurts when I breathe."

Jennifer sighed. "You got hurt pretty bad. It looks like my recovery is going to be a lot easier than yours, though you've been down this road before."

"Many times," Elizabeth added with a smile.

"Well, it's all right. I've got _two_ doctors looking after me now." John stated.

Carson nodded and smiled. "Right, though I'm not sure I'm ready to resume all my regular duties."

"Oh come on," Jennifer protested. "You are the rightful CMO of Atlantis."

Elizabeth smiled and held up her hand. "We'll talk about this later you two."

Carson and Jennifer both nodded and then took their leave. Elizabeth then sat at the edge of John's bed and took his hand. "Before I came down to see you, I had a check in with the IOA. They had just gone over my preliminary report."

"And?"

"And they thought that I handled the situation commendably." Elizabeth answered. "I took everything in stride and I managed to keep all my people alive. Overall, they're quite pleased and a hundred percent confident that they made the right decision to send me back in charge rather than Richard Woolsey."

John made a face at that. "I've been told about a future with him in charge. It did not go well," he paused and sighed. "At least we know that things are up in the air."

"Yeah," she agreed with a smile. "They always are, aren't they?"

John nodded and brought Elizabeth down so that she could lay next to him on the infirmary bed. "Welcome back Elizabeth," he stated warmly as he laid a kiss on the top of her head. "It's good to have you back in control."

_A/N- Another two chapter rewrite. Don't get used to them beloved readers. And as you can see...the name of the story has changed. Please leave a review and lemme know what you think of the changes I am making. _


	26. Part II: Ties to Fix

**Chapter Five: Ties to Fix**

Things were off. While off world Teyla and Ronan were attacked and Teyla returned home to Atlantis alone. Instantly, Elizabeth called a meeting and she along with Rodney and Teyla made their way to the conference room and sat down. "I've just gotten word from the Daedalus," Elizabeth began. "They've confirmed the results of your preliminary search John. There is no sign of Ronan's subcutaneous transmitter anywhere on the planet."

"That means he's still alive," John stated.

"How do you figure?" asked Rodney.

"If Tyre wanted Ronan dead, we would have found a body."

Elizabeth nodded at John's analysis. "I agree, but we have to face the possibility that Ronan could be in some serious, serious trouble."

"And yet he didn't kill me." Teyla interjected. "It would have been safer for him to leave no witnesses, so perhaps -- despite what the Wraith did to him -- Tyre still possesses his Satedan sense of honour.

Rodney shook his head. "It didn't stop him from ambushing you."

"We can use that "Satedan sense of honour" to help us find Ronon," John suggested, he turned to look at Elizabeth who raised an eyebrow. Her silent communication for '_how'_. "If we get a Satedan to help us then we might have a chance."

"You happen to have one handy, do you?" asked Rodney.

John shook his head. "No, but Teyla know where one is."

Teyla nodded. "Solen Sincha. He is a survivor of the Wraith attack on Sateda. Ronon and I encountered him on a trade mission to Belkan two years ago."

"Judging by your description, he isn't exactly the settle-down kind of guy. I mean, what are the chances he's still gonna be there?" Rodney stated pessimistically.

"There's only one way to find out," John stated and with that he, Teyla and Rodney got to their feet. Elizabeth was quick to follow and before heading to the doors John turned to her. "Do we uh, have permission to go off world?"

Smiling Elizabeth nodded and followed them into the control room. "Teyla?" she asked as John and Rodney headed down the stairs. "Are you going to go with John and Rodney?"

"I was planning on it," Teyla began uncertainly.

"But will you be returning full time?" asked Elizabeth. "You haven't let me know, and the IOA wants to know…."

"Well of course she'll be returning," John stated as he turned to Teyla. "Right?"

Teyla avoided his eyes. "I have yet to make a decision."

"Oh," John stated surprised. "Alright then."

"But I would still want to accompany Colonel Sheppard and Doctor McKay to Belkan," Teyla stated. "If that is alright with you Elizabeth."

Elizabeth nodded in understanding. "Ronan is your friend, he's a part of his family, and of course it's alright with me." She paused and watched as Teyla smiled appreciatively back to her. Then after catching John's eye she watched as her fiancée and his team made their way to gear up.

—sparky—

Later, much later while Elizabeth was continuing to unpack her stuff into her office, Teyla came to visit her. "Elizabeth?" she asked tentatively as she stepped through the doorway. "Can I talk to you?"

"Of course," Elizabeth stated as she motioned for Teyla to sit down. "Has there been any word on Ronan yet? I heard from John that you had another lead…"

Teyla shook her head. "Unfortunately not…"

Elizabeth sighed. "Well I suppose we can draw comfort from the fact that he is a proven survivor. He defied the odds for many years as a Runner," she began thinking that the situation with Ronan was what was getting her so down. "He'll be alright."

"I believe that he will," Teyla agreed. "At least I hope that he will, but that is not what I wanted to come and talk to you about."

"It isn't?" asked Elizabeth.

Teyla shook her head. "No. I wanted to apologise for not having come to you sooner with a decision regarding my position on John's team."

Elizabeth smiled sympathetically. "Take whatever time you need. If necessary, I can assign someone to fill in for you…and I am here if you ever need to talk."

Teyla shook hear head. "It is just that I do not know what to do. This is so difficult for me. For most of my life, I never imagined the possibility of leaving my people, not even for a moment, and then circumstances changed. And after realising a far more important role on Colonel Sheppard's team, I never imagined the day would come when I would have to let it go. Now here that day is."

Elizabeth smiled compassionately. "I understand," she stated softly. "I never thought that my priorities would change past being a diplomat on earth, taking care of my dear Sege and planning a future with Simon, the man I was with at the time," she paused and fingered the engagement ring on her hand. "Now, I'm in a whole other galaxy, engaged to one of the most selfless men that I have ever met and even though I'm technically only half of who I was before…I wouldn't have it any other way for my new priorities fulfil me more than I ever imagined. Priorities do change."

"And sometimes they don't," Teyla replied thoughtfully.

Elizabeth nodded. "Sometimes they don't. Listen; if you're worried about Kannaan, I'm sure that he will support you in whatever decision you make. He's the father of your child and he only wants the best for both of you."

"Yes," Teyla agreed with a smile. "Of course he will, thank you Elizabeth."

—sparky—

They had heard of a lead for Ronan. John along with Rodney and Lorne's team were geared up as they entered the gateroom. Elizabeth stood over the balcony and watched as they walked towards the gate. "We'll get him," John called up to her. "We'll bring him back."

"See that you do Colonel," Elizabeth called back putting on her 'leader' face knowing that in a situation such as this she had to let him know that he was a Colonel with no personal ties to Atlantis. He had to be focused to get to Ronan and he wouldn't be able to do that if he was thinking of her. "Be safe," Elizabeth added and with his dear smile, John without words promised her that he would be safe."

—sparky—

They didn't find Ronan, but they found an even better lead and as he was detoxing, John spoke to Elizabeth about Teyla on their balcony. "Has she talked to you?" he asked curiously.

"Teyla?"

John nodded.

"Yes she has."

"Has she decided?"

Elizabeth shook her head. "No she hasn't," she paused and took John by the hand. "She wants to rejoin the team John, she really does. She hasn't said as much but she still feels the same obligation to fight by your side, to defeat the wraith and keep her people and the rest of the humans in the galaxy safe. But her priorities have changed. She has a baby now and she has to think of him, and his father….." she paused again and leaned into John's shoulder. "You're going to have to face the same choice too one day."

Understanding, John said nothing but mulled the thought over. Elizabeth was right, one day if all went well the two of them would have a child and he would have to make the same choice. Would he still continue to go through the gate, even though he had a family waiting for him? Could he really risk leaving his child and his wife behind to mourn him? It was something that John had never had to face before and he wondered if he was ready to make that choice…and of course he realized that if he wasn't ready, then neither was Teyla; and he would have to be alright with that.

—sparky—

Tyre was conscious and John was making the case to Elizabeth that they let him go with the team through the gate. "It could be really dangerous John," Elizabeth stated in a low voice. "He could be leading you into a trap."

"He could be leading us to Ronan," he stated firmly. "It's worth the risk,"

After taking a couple of deep breaths, Elizabeth nodded. "Of course, be careful."

"What is it?" asked Teyla as she walked by them. "What is happening?"

"We know where Ronan is," John stated.

Teyla's eyes widened. "I'm coming with you."

John nodded. "Gear up,"

'Teyla?"

Teyla turned to her friend and handed Torren over to Elizabeth. "I was about to meet Kanaan in the cafeteria. Would you please explain to him the situation?"

Nodding, Elizabeth took the baby. "Of course I will." And with that she watched as Teyla fled down the corridor after John. Torren moved in her arms and Elizabeth held him a little more securely. "It's alright little one," she soothed. "Your mommy is just going to go get your Uncle Ronan back from the bad guys. She'll be back soon."

—sparky—

"So is Ronan alright now?" asked Elizabeth much later as Ronan was resting comfortably after going through his own detox.

Carson nodded. "Aye lass," he stated. "Physically he's still weak, but his blood work shows no traces of the enzyme in his system, so he should be back to his old self in no time."

Jennifer nodded. "He's amazingly strong, he made it through on shear will power," she sated with a smile. "He'll be back to active duty within a week or so, just to be safe."

Elizabeth nodded in understanding. "Very well. We've all had a trying couple of days. Let's get some rest."

Carson, Jennifer and Rodney instantly got up and left the room, but Teyla remained behind catching John and Elizabeth as they were about to leave. "John, Elizabeth?"

"Yes?" asked Elizabeth as she turned towards her friend.

"I have come to a decision," Teyla began. "I would like to rejoin the team."

John smiled. "It will be nice to have you back,"

"I'll feel better knowing that you are watching his back," Elizabeth agreed.

And with that, the three of left the control room, another crisis adverted.


	27. Part II: While You Were Gone

**Chapter Six: While You Were Gone**

"Rodney," Elizabeth chastised as she, Rodney and John left the Conference Room and headed towards the control room. "Come on now,"

"What is he talking about?" asked John, who had only been half listening to the conversation between the man who was practically his best friend and his fiancée.

"She's hiding him from me," Rodney protested.

"She's not hiding him," Elizabeth insisted. "She isn't."

"Oh yeah?" asked Rodney. "Every time I go to see him, she tells me that he's just settled down. Me, the person who helped give birth to the little guy. The one he should have been named after."

"You're not still sore about that are you?" asked John with a fake wince. "It's not like I asked her to give her son, my name."

"And can you blame her?" Elizabeth stated. "You did drop him."

"That's right," John agreed. "There's that."

"I did not drop him," Rodney insisted. "He jumped."

"_Jumped?!_" asked Elizabeth and John together as they shared a look.

"Well," Rodney began with a sigh. "He wiggled out of my arms. Loo, I said that I was sorry. Besides, how much damage could I possibly have done? He fell, like, maybe two feet. Stuff like that happens all the time. I was dropped like a dozen times when I was a kid."

"Well, that explains a lot," John teased as Elizabeth held back a childish giggle. "Why do you even care?" he continued. "You don't even like kids."

"Well it's the principle of the thing," Rodney explained. "Everyone else gets to hold him—why shouldn't I?"

"Colonel, Ma'am," began Chuck as he sat at his console. "We got a new contact. It looks like a ship."

"How far out?" asked Elizabeth, that nervous tense edge to her voice.

"It's in orbit," Chuck answered.

"Well, how come we didn't detect it?" asked John.

"I don't know," Chuck admitted. "We didn't even detect the hyperspace window. It just appeared out of nowhere."

"Hang on a second," Rodney began as he looked at his machines "We're getting I.F.F. It's the Daedalus!

"Daedalus?" asked John. "How can that be? They're on their way back to Earth."

"Well they are," Elizabeth began as she turned to Rodney. "Rodney?"

"Opening a channel," Chuck stated as he activated the appropriate controls.

"Daedalus this is Atlantis," John began. "Please come in."

There was no reply.

"Steven?" asked Elizabeth. "This is Elizabeth, please respond."

"They're not going to answer," Rodney interjected.

"Why not?" asked Elizabeth

"Cause I'm not reading any life signs." Rodney answered.

"What are you telling me, Rodney?" John began, "This thing flew here by itself?"

Rodney shrugged his shoulders. "I don't know how they got out here," he began. "But there's no-one on board. At least, no-one alive."

—sparky—

"John," Elizabeth began as she caught up with her fiancée as he was heading to the jumper bay. "I-"

"I know," John interjected with his usual smile. "I'll be careful."

—sparky—

"John," Elizabeth stated into a microphone about ten minutes later. "We just got confirmation from Stargate Command. The Daedalus is in the Milky Way, on course and on schedule. They expect to reach Earth in two days."

"Understood," came his reply and then Elizabeth could do nothing but wait.

—sparky—

"John?" Elizabeth asked about twenty minutes later. "John this is Atlantis. Radek has picked up some kind of power surge coming form the ship."

"Yeah," John replied. "We noticed it. We're trying to check it out ourselves"

"Their levels are still rising," Radek pointed out, noticing as Elizabeth's face tightened.

"Colonel?" asked Lorne as he stepped in. "Should we send another Jumper to assist?"

"No," came John's reply. "Stand by…"

After two long minutes, there was no reply and Elizabeth walked to the edge of the balcony overlooking the gate trying to get a signal. "John do you read?" she asked. "Daedalus this is Atlantis please respond…"

"What the hell is going on?" asked Lorne as he turned to Radek.

"I don't know. One moment they were there and the next minute, they were gone."

"They can't just be gone," Elizabeth insisted. "Where are they?"

"I—I—"

"Radek,"

Radek sighed. "I don't know Elizabeth," he answered honestly. "The only thing that I can think of, which is consistent with the lack of readings before the ship appeared on sensors is that it came from an alternate reality."

"Alternate reality?" asked Lorne, not really believing it.

"We've seen it happen before," Radek answered.

"What does this mean?" asked Elizabeth, changing the subject. "What can we do?"

"Unfortunately nothing," Radek stated sadly. "I hate to say this Elizabeth, but if they're going to make it out of this, they're going to have to do it on their own. We know of no way to track them."

"There has to be a way," Elizabeth insisted, but Radek just shook his head. Then, taking a deep breath, Elizabeth turned on her radio and tried to get in touch with them. "John this is Atlantis, please respond…John this is Elizabeth, if you can hear me, please respond…John…"

—sparky—

Later, much later Chuck picked up something else. "Another contact just appeared on our screens."

"Is it the Daedalus?" asked Elizabeth, desperation evident in her voice.

"They're too far out to get an IFF," Radek answered.

"Colonel Sheppard do you read?" asked Lorne.

"John?" asked Elizabeth a immediately after him. "Can you hear me?"

"Was there a hyperspace window?" asked Lorne.

"No sir," Chuck answered. "They just appeared out of no where."

"It's gotta be them, 'Elizabeth stated anxiously. "Major Lorne, take a Jumper."

"Aye Ma'am," Lorne said. "Doc," he continued. "You're with me. Let's go."

—sparky—

"So what was it like?" asked Elizabeth that night as she and John relaxed in the mess hall.

"Odd," John answered, almost distantly.

"And Rodney?" she asked again, trying to prompt him into conversation. "He was asleep when I got down there."

"He's fine," he answered again.

"John?" Elizabeth asked as she took his hand. "Are you alright?"

"Just tired." He answered stoically. "I'm going to get some rest."

Elizabeth sighed. "Then I'll catch on work…" and with that she watched him go. _What is wrong with him?_ She wondered. _What happened out there to make him so...distant._ Little did she know, that she would soon find out.


	28. Part II: Ghost of the Past

**Chapter Seven: Ghost of the Past **

_"Uh listen," asked the other John Sheppard in the F302 or at least its equivalent. "I know that this is going to sound really, really strange but do you uh- do you have your Elizabeth with you?"_

_"Well she's not here on this ship," John replied as he sat in his chair aboard the Daedalus. "But she's back at our Atlantis…why do you ask?"_

_"No reason," John, the other John replied with a tightness in his voice that made the John on the Daedalus wonder what had happened that was so bad. "I was just wondering…"_

—sparky—

John was walking along the corridor when the lights begin to flicker. "Rodney?" he asked. _"Go Ahead,"_ came the response over the radio. "Are you messin around with the power again?" John asked irritably. "The lights are flickering."

"Yeah," Rodney agreed, though John couldn't tell if that was a 'yes I'm to blame,' or a 'yes I know what is going on' kind of tone. "I'm getting reports from all over the place…" Rodney trailed off as the lights began to flicker on and off. "Hello?" he asked, though he got no response.

John, continued walking along the corridor while the lights continued to flicker on and off, then ducks back as an electrical bolt surges between the walls just in front of him. "Rodney??" he asked although he got no response.

—sparky—

In the control room, Rodney and Radek were working on the consoles as John came up the stairs. "Hey," he stated as he spotted Rodney. "I tried to radio you."

"Yeah," Rodney agreed with a sigh. "Communications are down."

"Yeah obviously," John responded. "What's up?"

"We're working on it." Rodney replied.

"Well, I just almost got zapped by a bolt of lightning." John pointed out as Rodney looked up in surprise.

"What?" he asked. "Displacement current? Here?"

John nodded. "Yeah, right there in the corridor, just like the one we had in the Jumper."

"So, _not_ a coincidence." Radek stated as an alarm beeped.

"We just lost power to the Stargate." Chuck reported.

"What?" asked Rodney.

"Maybe a virus uploaded itself or something." John suggested.

"No-no," Rodney protested. "I disabled the Jumper's network connection for this very reason. There is no way the anomaly jumped to the city's systems." Then suddenly, a huge bolt of lightning surges across the room and hits one of the consoles. Everyone cringes, then looks in shock at the shattered screen of the console.

"You'd better figure it out, because whatever was in that Jumper is now in the city." John stated grimly.

—sparky—

Deep asleep, John tossed and turned having a horrible, horrible nightmare.

—sparky—

It was night time on Atlantis when Richard Woolsey walked into the Control Room. "Where've _you_ been?" asked John.

"On the other side of the city." Woolsey replied. "A transporter malfunctioned and sent me to the East Pier. I had to walk all the way back." He paused and looked pointedly down at Chuck, who takes the hint and vacates his chair so that Woolsey can sit down.

"We've got power disruptions all over the city. Look, nearly every system's affected." Rodney stated as he continued to work."

"We think whatever's wrong with the Jumper has infected Atlantis." John suggested.

"It's one of several possibilities we're looking into." Rodney interjected.

""Several"?!" asked Radek in disbelief as it was their only idea.

"It's a possibility, all right?" Rodney stated snippily "Look, the point is, we have no idea what's going on here."

"I was almost hit by a bolt of lightning." Woolsey stated.

"Join the club," John stated sarcastically.

"Look," Rodney explained. "The energy builds up in one area and then discharges in a high-voltage displacement current. Very erratic, and very lethal."

"I tried to radio you." Woolsey stated tiredly.

"Yeah, well, communications are also down." Radek answered.

"So's the Stargate." John added.

"We can't dial Earth?" asked Woolsey almost terrified.

"Don't worry, all right? I will figure it out." Rodney assured. "I've just gotta run a few diagnostics, narrow down the…" he was cut off as all the lights went out and the computers powered down. The Control Room was plunged into darkness and Rodney could feel his heart sinking.

"Well, _that_ can't be good." John said, stating the obvious."

"OK, OK. We need to organise some teams, fan out through the city, keep everyone calm until we figure out exactly what the…" Woolsey stopped as a small light comes on. Rodney stares at the computer in complete and utter surprise.

"Hey, the laptop just booted up." Rodney pointed out.

"It's probably just the battery." John suggested.

"No-no-no-no, it's drawing power from the system." Rodney answered.

"So everything's out except _your_ computer?" Woolsey asked suspiciously.

Rodney rolled his eyes. "I am as confused as you are."

Then, text began to scroll across the screen. At first it was all gibberish, but it eventually settled into a pattern reading _…alm ... shukrsh ... fhazzr .. dsttuhe ..._

"What is that?" asked Woolsey.

"Looks like some kind of a code." John theorised.

"Maybe," Rodney agreed.

"Could be a message," Radek suggested.

The text then altered itself and became longer, as though it was responding to what Radek stated. None of it however made any sense what so ever. As it took itself to the second line, some of it deletes until the second line reads only…_hle_… It then deleted itself and became _hel_ after which _hlepp_ and then finally _help_.

"Help?" asked Woolsey in compete shock

Rodney leaned over and began to type… _Who are you_. The computer replied, constantly changing and correcting itself as though it was learning how to use the Atlantis system. Finally it settled on two words, though John had it figured out long before the computer itself had. _Elizabeth Weir_ it stated. And everyone stared at the screen in complete shock. "Doctor Weir?" asked Woolsey. "But she's dead."

John who felt as though his world was falling apart could barely talk. "So we've been told….."

—sparky—

Later, Radek finished tweaking a wall panel. "Right," he stated as he activated his headset. "Rodney…Rodney? Rodney, come in. Rodney, can you hear me?"

"Go ahead," he replied over radio.

"I've completed the patch. Go ahead and try it whenever you're ready." Radek stated knowing that in Rodney's lab some questions were about to be answered. There, John, Rodney, Teyla, Ronan and Woolsey were there. "Okay," Rodney stated. "Fingers crossed."

"What are you doing?" asked Rodney

"Well, whatever this entity is, it's completely overwhelming the city's systems. Now, it's spread out. It's like dozens of fragmented programmes that are fouling up power management, communications -- you name it. Now, I've managed to merge them, to patch them together into one incredibly large programme that will (a) hopefully render our systems slightly more stable and (b) allow us to better communicate with whoever or ... whatever is that's claiming to be Doctor Weir."

After a question by Woolsey, they finally started to get some answers. "I'm sorry to cause all this trouble. Who's there with you? Is -- is John Sheppard there?" asked the computerized voice that sounded so far from Elizabeth's light-hearted voice.

John hesitated for a long time before he decided to speak, and when he did it was quiet and nervous. "Hi," he stated wondering what the computer's response was going to be.

"It's so good to hear your voice again." The computer responded and John could almost imagine that it was Elizabeth speaking.

"We, uh ... thought you were ... dead." John stated, not knowing quite what he was saying.

"I suppose I am -- my ... my physical body, anyway, but my consciousness is still intact." The computer explained.

"Right. So, um, what happened?" asked John.

"Do you remember the day I ordered you to leave me behind?" the computerized voice asked and John had a flashback to the moment when Ronan and himself found Elizabeth in the corridor on the Replicator Homeworld with the enemy shooting at him. _Come on,_ Ronan had stated. _Elizabeth!_ John had called out in anguish. _Go!_ Elizabeth had ordered, an equal amount of anguish in her voice. John caught one last glimpse of her pained face as the Replicators surrounded her, seized her arms while John and Ronan escaped around the corner. "Yeah," John answered quietly. "Yeah, I remember."

Elizabeth, or rather the computerized voice of Elizabeth explained how the Replicators had then taken her to a lab and allowed her nanites to replicate and therefore make her fully one of them. She explained how she was sent into the city in her new form, but still as her self. She told of how the remnants of Niam's group found her and how he had run into some of their handiwork, the human versions of herself and the rest of John's team and how she had learned of it after everything had gone down. Elizabeth explained how the leaders of the group wanted the other Elizabeth to believe that she was the only one, and John figured it was to stop them or rather him specifically from coming after his Elizabeth.

"This is all very interesting, I'm sure, but none of it explains how you've come to be a disembodied voice in our computer system." Woolsey interjected.

"Is that…Richard Woolsey?" asked the computer voice.

"Uh yes," he began as he cleared his throat nervously. "It is. Uh, I'm the, uh, the-the new ..."

"The new you," John explained.

"I see," the voice stated quietly, and John could again picture the displeasure on Elizabeth's face and although he was almost afraid to ask he did ask as to what had happened after. She explained how they were on the run and how Oberoth was hunting them down. She then told of the miracle of the destruction of the replicator homeworld. John explained how it hadn't been a miracle, how it had been them. Elizabeth responded that she knew and she was grateful for it allowed her and her new people to work towards their goal of ascension.

She explained how they had landed on a planet and how they had began to mediate, but how it had been very, very difficult because they were machines. After some quips by Rodney she continued with how they had eventually found a way to project their consciousness into subspace but how that had not been the next step at all. They had been trapped, wandering from one technologically advanced society to another searching for a solution. "I didn't know where else to turn," she concluded. "You're the only friends I have."

—sparky—

Knowing that she had to act quickly, Elizabeth built herself a body using the last template that had been created. She was herself, but she didn't look like herself and when the doors to the lab had opened, she had known that. "Hello," she had stated as weapons were pointed at her. The group moved inside the lab, the weapons still pointed at her while Rodney checked her over with the equipment that he possessed. "Listen to me," she tried to explain in a voice that was not her own, looking through eyes that were not her own. "I'm Elizabeth Weir."

"Obviously she was in a hurry. She just used the previous Replicator template that was already in the machine ... which was FRAN." Rodney stated.

"John," Elizabeth began in the voice that she so often used with him. "I'm not a threat to you…." And in the end she wasn't. While the others of her kind could not be trusted in the construction of organic selves, she suggested a solution that would solve everything

"You can't do this," John protested as he caught her by the arm, finally knowing after she saved his life that it was Elizabeth—his Elizabeth. "There has to be another way."

'Elizabeth' shook her head sadly. "No John," she answered softly. "There isn't."

"I'll come get you then," he stated. "I'll come in a jumper and…"

'Elizabeth' raised a finger to his lips to silence him and then using what little advantage Rodney had given her she morphed into her actual self. "I have to do this John," she stated quietly. "You know it."

Shocked at seeing his Elizabeth before him, with the face he remembered and the eyes he remembered John wrapped his arms around her tightly and was not shocked when she returned the embrace. "I can't lose you again…"

"You already lost me," Elizabeth stated sadly as she buried her head into the crook of his neck. "At least this time," she continued her voice choking up with an emotion that she could no longer really feel. "At least this time we get to say goodbye."

John shook his head and pulled back. "I don't… I can't…" he paused and took a deep breath. "I can't say goodbye to you Elizabeth, I just can't."

"You have to."

"Why?" he asked not wanting to let her go. "Why should I?"

"I have to solve the problem,"

"Damn the problem," he protested. "If Woolsey is willing to let you guys stay here and continue your work then you should stay and continue your work….damit Elizabeth you could come home. Are you really willing to walk away from everything…from me?"

Elizabeth blinked a couple of times in shock before reaching up to touch John's stubbled cheek. "Walking away from you is the last thing that I want to do," she answered honestly. "But I have a responsibility to this city, its mission and its people. I have to keep them safe."

"That's my job," he protested quietly. "Let me do my job….let me save you."

Elizabeth shook her head. "This time you can't."

"I'll find a way," he promised as he took her hands within his own. "I'll find a way to come and save you—god Elizabeth I swear to you that you won't be frozen out there forever. I'll find a way to rescue you…to bring you home."

Elizabeth smiled softly and John could almost swear that there were tears in her eyes, though it had to have been a trick of the light. "I know you will," she answered slowly as she reached up and kissed him softly on the lips. "You've always been my hero…"

—sparky—

John woke up in the dead of night, startling Elizabeth who had settled down beside him. "John?" she asked sleepily as she looked at the terror an panic on his face. "John?"

As the remnants of the dream faded, the realisation of what could happen hit him. "I have an idea," he stated as he turned to his fiancée. "I have an idea…"

"What kind of idea?" Elizabeth asked as she watched as John looked at her. "John?"

"An idea to turn you human," he explained as he wrapped her in a tight hug. "An idea to keep you with me forever…."


	29. Part II: Losses and Gains

**Chapter Eight: Losses and Gains**

"Rodney?"

"Working."

"Rodney?"

"Working."

"Rodney!"

"I'm working on it!" Rodney shouted as John pestered him for what felt like the thousandth time that afternoon. "You know, I know that this was your idea but honestly, I'm…" he paused and bit his lip as he realized what he was about to say.

"Not as smart as a replicator?" Elizabeth asked with a wide smile. "Come now Rodney, you're the smartest person in two galaxies I'm sure that you'll figure it out."

Rodney just shook his head. "This idea came from a dream…."

"Nightmare's more like it," John clarified. "But can it work? Can it turn her human?"

"Using the machine to create human cells instead of nanites is a lot easier said than done," Rodney pointed out in aggravation. "I mean honestly I don't know if you can do this."

"You have to," John stated. "Elizabeth's life depends on it."

"My life is fine right now thank you very much," Elizabeth countered.

"You're still half replicator,"

"And half human," Elizabeth insisted. "I've been over this before."

John sighed. "I know that but if this can make you fully human again…"

_Elizabeth Weir, this is the control room…_

"Come in Control Room," Elizabeth stated, interrupting John.

_You wanted to be informed when the deadline was past. _

"Doctor Nichols' team hasn't checked in yet?" asked Elizabeth.

"The team studying global warming?" asked Rodney in a whisper.

_Yes Ma'am. He's an hour over due. _

"Understood," Elizabeth confirmed with a nod as she turned towards John and Rodney. "I have a new mission for you both and the rest of your team."

—sparky—

"John," Elizabeth called as she stood on the balcony overlooking the gateroom. "Please tell the research camp that I'm not a happy camper when my people don't check in."

"Do you want us to _smack_ him around or anything?"

Elizabeth laughed. "No. Just remind him…." she paused and looked at the nervous look on Rodney's face. "Don't worry Rodney," she assured. "I'm sure that Katie's alright."

Nodding absentmindedly Rodney said nothing as they went through the gate. _Please let the team be alright,_ Elizabeth prayed silently. _For Rodney's sake…_ She was just about to go to her office and catch up on some paper work when suddenly the gate started to dial and the alarm sounded.

"Unscheduled off-world activation ma'am," stated Chuck at the controls.

"Activate the shield," Elizabeth ordered as she ran to the balcony as the shield came on and the gate activated. "Is there an IDC?" she asked, seeing how Chuck shook his head.

_Atlantis, this is Sheppard,_ came the voice of her fiancée and military leader of the Atlantis expedition. _Do not lower the shield. The entire tower will be flooded._

"Flooded?" asked Elizabeth. "What the hell is going on John?"

_It's cold and wet._ John answered over the radio. _The Stargate's under water. The entire valley's flooded._

_And it's freezing!_ Rodney added.

_Elizabeth, you need to send a Jumper through so we can stay warm and dry until the water recedes._John stated.

"Will do John," Elizabeth promised. "Hold on…"

_Holding on Elizabeth,_ John assured. _Sheppard out. _

Moments later the jumper was in position but the gate wasn't disengaging. "John?" asked Elizabeth. "The gate…"

_It's the water._ Rodney answered over the radio. _The constant pressure's forcing the wormhole to stay active, which means we're gonna have to wait the maximum amount of time a Stargate can stay open -- thirty-eight minutes._

"That's thirty-two minutes you guys," Elizabeth answered. "Can you hold on?"

"We will endure," Teyla assured.

"I can't stop shivering," Rodney complained once the radio communication with Atlantis had been cut for the time being.

"You're letting all the hot air out of your mouth." Ronan pointed out.

"We'll be warm soon enough," John promised as Rodney shivered.

"I don't know," Rodney complained. "I think I got wetter than you."

"I don't know -- I got a little damp dialling the D.H.D." John stated sarcastically.

"The research camp was further up this valley. I'm a little concerned for Dr Nichols' team, and Katie," Teyla stated.

Rodney's eyes widened as the full reality of the situation hit him.

"Anyone at the research camp, this is Colonel Sheppard. Please respond." John stated over his radio even though there was nothing but static in response. "I repeat: this is Colonel Sheppard. Please respond."

Rodney shook his head, trying to fight back his tears as well as his shivers. "I'm pretty sure they're all dead."

"We can't know that, Rodney." Teyla stated.

Rodney shook his head again. "Look, the research team was studying the effects of global warming. They set up camp at the foot of a massive glacier up the valley."

John sighed heavily. "You're thinking the ice dam broke."

"Right. I mean, the Ancients don't put Stargates on a flood plain, and I certainly don't think the tide just came in. That's probably why the water's so freezing." Rodney answered as he sneezed. "Oh! Oh, OK. OK, so now I'm hot _and_ I'm still shivering."

Teyla put her hand on his forehead. "Were you running a fever before we left?"

Rodney shrugged as best he could. "I dunno. Maybe. I'm always running _something_…" he trailed off and whimpered in pain.

John looked down and closed his eyes. "So the water's receded a little bit, but uh it looks like we're—"

"We're gonna be stuck here all night." Rodney finished.

"In the back of a warm, cosy Jumper, all right? All you need to do is hold on for -- I don't know -- thirty minutes or so." John added, hoping beyond hope that things would be alright.

—sparky—

In the morning, Sheppard and his team hurried through the gate into the gateroom of Atlantis. Ronan was carrying an unconscious Rodney in his arms who was wrapped in a blanket. A medical team was waiting, as was Elizabeth and all watched as Ronan laid Rodney down on the gurney. "How long has he been unresponsive?" asked Jennifer.

"Since he fell asleep in the Jumper -- about nine hours." Teyla answered.

"Okay, let's get him to the Infirmary. I want him under a scanner," Jennifer paused and looked at the rest of the team. "I wanna have a look at you guys too."

"We're good." Ronan assured.

"By that, I mean now." Jennifer countered as the medical team wheeled Rodney away with the others following. Elizabeth took the opportunity to fall into step with John

"Why didn't you return in the Jumper I sent you?" she asked.

"I ordered the rescue party to continue the search for Nichols' team. There's a chance they're still alive…." John answered. "They have to be, for Rodney's sake."

Nodding with full understanding, Elizabeth stayed silent.

"I'm gonna go checked out and then I'm gonna check on Rodney," John stated and with that he disappeared around a corner. He walked to the infirmary and found Jennifer at Rodney's bedside. She wasn't standing over him in the way that a doctor usually would, she was sitting on the edge of the bed, holding his hand like a friend. And John knew why she was doing that.

"Well?" he asked, trying to keep his voice light as he walked over to Rodney and Jennifer. "How's our boy?"

Jennifer sighed, stood up and picked up the clipboard with Rodney's information on it. "He has no fever and no hypothermia…nothing on the scan at all."

Rodney looked around and watched as Teyla and Ronan joined them. "What about you guys?" he asked. "None of you hurt? You're all okay?"

"Yeah," John assured. "We're good."

"What about you Rodney?" Teyla asked softly. "Will you be okay….?"

Rodney took in a shaky breath and nodded. "Yeah—of course I will. I uh—I don't suppose that you guys found Katie while I was unconscious because I uh…." Rodney paused as he looked at his friend's faces. "…I didn't think so."

"I'm going back out there to lead the search myself buddy," John assured as he patted Rodney on the shoulder. "So you just concentrate on getting better."

"I am better," Rodney insisted. "I want to get back out there."

"No." Jennifer ordered. "No you're staying right here. I just want to make sure that you're okay."

—sparky—

But Rodney wasn't okay. He seemed to be getting better, asking for food and everything but when Elizabeth showed up with her 'I'm sorry' face he seemed to change drastically. Even when Elizabeth brought him to see the body he didn't quite know what to do with himself. He just sat there, for endless hours watching and wondering what could have been. And only Carson could pull him out of it.

"She's at peace now," he stated quietly not wanting to disturb Rodney anymore than he had to. "She's not in pain anymore."

Rodney said nothing. He was silent as a stone like he had been for hours. Carson waited for a couple of moments before turning to leave. That's when Rodney decided to talk. "You don't suppose that she thought of me do you?"

"Pardon?" Carson asked, not quite catching the question.

"I mean if it was me I would have been too self-absorbed with saving my own skin to think of anyone else," Rodney stated his voice rambling and his tone verging on the breaking point. "I mean drowning must be a horrible way to go, not being able to breath but so much more painful then suffocation…but then, Katie wasn't selfish like me so I wonder if she thought about me in those last few minutes."

"Rodney—"

"I mean, she said that she loved me so it would make sense that she would think of me right?" Rodney asked still rambling. "I mean we were going to be married soon. We were making plans and everything. She told me just last week that her sister had sent her this gorgeous picture of a dress and she was going to look at it the next time we get back to earth…" he paused and turned to Carson. "It was going to be a winter wedding you know, at Niagara Falls. She loves—loved winter so much and she knew that I had never been to the Falls and how that bothered me. A small wedding. That's what we wanted, with friends and family. You and John and—and Ronan were going to stand up with me did you know that Carson?" Rodney paused again and shook his head.

"No of course not; how could you know that when I hadn't even asked you yet…I suppose now that it was better that I didn't ask you 'cause can you imagine the horror of having to return a three-hundred dollar suit?"

"Rodney—"

"I know what you're going to say Carson," Rodney snapped angrily as he strode past his friend. "And I don't want to hear it."

And from that moment on, things only got worse…

—sparky—

"My god—" Jeanie cried as she broke down in Elizabeth's office. "—how could it come to this?"

"Jeanie?" asked Elizabeth as she extended a tissue to the younger woman.

"How could my brother, my Mere be reduced to such a state?" she asked through her tears. "It just doesn't seem fair. You know? His mind was the one thing that he took pride in—that and his work which was always an application of his mind anyways but he was known for what his mind concocted like some mad scientist, only Mere saved the world a lot…"

"Ronan has a—"

"I know," she snapped. "I know that Ronan knows of a place and that that Doctor Keller is the one who's not letting him go. Carson, Carson's tried to reason with her but he's not your CMO anymore—not really and therefore he can't make the decisions."

"That's right." Elizabeth stated, her own voice wavering over the stress that she was under, and the thought of losing one of her dearest friends. "But Jeanie, you can."

—sparky—

And so the went though with Ronan's plan. They all went leaving Lorne and Zelenka in charge of the city for a few hours. It took time, but when they got to the shrine they got their Rodney back, in more ways than one. At first they weren't sure that they were going to be able to take him out of the shrine and then Jennifer and Carson together figured out what made the parasite within Rodney's brain retract and together they managed to extract the bugger while it was small enough—although they had help, the little bugger took itself away from the radiation and left Rodney's brain of it's own accord. Leaving him healthy once more…

However while his body healed, his emotions would take a little more time. Jeanie couldn't take the time and Rodney understood for his sister had her own life just like he had his…and it was a life that Jennifer helped him to recover. "Hey there," she stated as she brought him his breakfast one morning. "How are you?"

"Doing better," Rodney answered without his usual cockiness. "How about you?"

Jennifer smiled a little. "Alright I guess. No major issues in the last couple of weeks so Carson and I have had an easy time dealing with things."

Rodney nodded. "I hear that they've demoted you," he paused and winced at his choice of words. "That is to say that in the weeks since my uh little episode, the IOA has decided to put Carson back in charge as the CMO of Atlantis."

Jennifer nodded. "That's right."

"Does that bother you?"

She shook her head. "Nope."

"Why not?"

Jennifer shrugged her shoulders. "I love working here Rodney. I don't like being in charge. I messed up so much and—"

"—hey now," he interrupted as he reached out and took her hand. "You did save my life you know, that's a plus."

Jennifer looked at Rodney and saw the friendship in his eyes. In that moment she knew that their Rodney was back—changed—but back none-the –less and Jennifer was thrilled that her friend was coming back into his own and that he was asking for her help to make the transition back into his normal life.


	30. Part II: Whispers in the Night

**Chapter Nine: Whispers in the Night**

Laughter exploded all around them. It was the weekly women's card night which consisted of Dr. Elizabeth Weir, Teyla Emmagen, Dr. Alison Porter and Jennifer Keller. The three of the four women had been meeting on a regular basis for quite a long time, but with the loss of Katie Brown, none of them had wanted to replace her. It had been the young plucky doctor who had suggested that they start up a poker night—and thus even though it wasn't the Euche they were used to, Elizabeth along with Teyla and Jennifer were playing and having a great time.

"So tell me Alison," Jennifer began between rounds. "The rumour around the infirmary is that Carson and you really hit it off a couple days ago—despite all the problems."

Alison blushed and hid her face behind the cards. "Did he tell you that?"

"You mean it's true?" asked Elizabeth watching Alison's face carefully. "Awe, you have a crush on Carson."

"And from what I hear, the feelings are mutual," Jennifer added.

Alison blushed even further. "Do not be embarrassed," Teyla stated as she placed a comforting hand on the young woman's shoulder. "Carson has gone through many hardships over the years—it is good that he has found someone."

"Oh I'm not sure that he's found someone," Alison defended as she looked over her cards. "I mean, sure we did hit it off but that doesn't mean anything…does it?"

Elizabeth laughed at the younger woman's innocence. "Trust me Alison, Carson doesn't 'hit it off' with just anyone. The last person…" she paused and thought back to their first year and the debacle that was the Hoffan Tragedy and the loss of Perna. "…the last person that he 'hit it off with' ended up dying before anything could come of it. That was five years ago. Believe me when I say that if Carson 'hit it off' with you then it is most defiantly a good thing."

With a smile, Alison filed all that new information away before she set her bet and played her first card, which caused the other three women to groan at the strong first card. It was going to be a long night of playing cards and Alison wondered how much information on Carson she could get from the women who knew him best. The girls talked for hours as they laughed and played and by the end of it all Alison felt that she knew Carson a little better, and she had an idea of what to do.

---

The following morning she found him working as always in the infirmary checking over this and that. Alison paused for a moment and smiled as he worked. He was so engrossed that she almost felt guilty for interrupting him—but in the end she didn't have to say anything, he saw her first. "Alison," he stated with a surprised tone in his voice. "What are you doing here?"

"Well I uh, I was hoping that you'd…" Alison paused in an attempt to calm her racing heart and shaky voice. "I was hoping that you'd like to have lunch with me today in the mess hall."

Carson just stared at Alison for a fraction of a second as he contemplated her offer. That moment passed and he just nodded smiling. "I'd love to lass," he replied watching as her face broke out into a grin.

"Great," she replied with a smile on her face. "See you at thirteen hundred then."


	31. Part II: Infiltrating the Enemy

**Chapter Ten: Infiltrating the Enemy **

"We received a message early this morning," Elizabeth began at the zero-seven-hundred briefing of her senior staff. Of all of them only Rodney looked to be half asleep. Teyla looked exhausted but Elizabeth knew that that had to do with her new baby. Ronan looked the same as always. Both Carson and Keller looked alert and cheerful and John, well a blush came to Elizabeth's cheeks as she thought of how much sleep _they_ got the night before. "The message was from Todd," she continued, putting the night before from her mind.

"Oh?" asked John with a raised eyebrow. "And what does he want?"

"What do you think he wants?" Rodney mumbled as he leaned his head against his hand. "He probably wants to trick us into doing something so that he can get his way and…"

"Actually he doesn't want anything." Elizabeth replied. "He heard of the blow that we dealt Michael and he wanted to know if we had learned anything valuable. I told him that we had made a breakthrough and he wants to meet with your team John to discuss it." Elizabeth paused and looked at the faces of her team. "I would have normally invited him here but he was set himself up in a hive within a larger alliance and while he can trust those immediately around him he doesn't trust everyone in his alliance despite his position and as a result as asked for you to come to him."

---

Seeing how there had been little discussion on the matter, John and his team which included Keller agreed to go meet Todd and just minutes before they were to leave Elizabeth pulled John aside into one of the unused jumpers. "I want you to be careful."

John smiled. "Aren't I always?"

Elizabeth narrowed her eyes. "This is Todd we're talking about."

"I have a relationship with him," he countered. "I know what to do."

"Still be careful," Elizabeth insisted as she kissed her fiancée. "I don't want anything to happen to you and I expect you back here in one piece."

John smiled and wrapped his arms around her. "I'll come back in one piece. Don't you worry about it all, okay?"

"I am going to worry," Elizabeth whispered knowing that in a matter of moments she would have to let him go as she did all the time. "I always worry."

"Well then you can worry enough for the both of us," John stated with a smile.

"And you don't worry enough," Elizabeth countered watching as his smile faltered and so she corrected herself. "No. You do worry. You worry about not coming back—"

"But I always do."

Elizabeth nodded knowing that there was nothing more that she or he could say on the matter. "Yes you do," she replied. "So I expect you to this time."

---

He did come back, but with a very strange request from Todd. "This is crazy," Elizabeth pointed out as she and John and Teyla sat within her office. "I mean come on Teyla do you realize what he is asking you to do?"

Teyla nodded. "I do and Doctor Keller and Carson assures me that the procedure is completely reversible and will have no lasting ill effects."

John shook his head. "We're not talking about the procedure."

Teyla sighed. "I know."

"Even if this does work," Elizabeth continued sadly. "even if all the Wraith stop feeding, you think they're gonna become nice and friendly overnight? No. They're gonna have a massive technological advantage."

"You're suggesting they will enslave the people of this galaxy rather than feed on them." Teyla replied.

John nodded. "We've seen the same thing happen in _our_ galaxy."

"You didn't voice this objection before," Teyla pointed out.

"Nobody was asking _you_ to risk your life." Elizabeth countered. "This could be very dangerous Teyla. You do understand that."

"I do." Teyla assured. "But my Wraith D.N.A. makes me the only possible candidate. Anyone else would be detected by the Queen immediately. This may be the only time we can do this and therefore we do not have a choice. We have to try for the sake of the galaxy and I have to try for the sake of my son." Teyla paused and looked to Elizabeth. "Please."

Elizabeth sighed and nodded. "Very well, we go with the plan."

"Elizabeth—"

"We go with the plan John," Elizabeth interrupted. "We started this a long time ago. Now let's try to finish it okay?"

John paused and thought back to what she was referring to and indeed it was high time for the expedition to complete the little experiment that had started with Michael. And in the end it worked—sort of. With the help of Teyla, Todd managed to get in control of his alliance and as Elizabeth went through the mountain of reports a few days later she couldn't help but wonder if she had made the right choice…


	32. Part II: Restoring the Lost I

**Chapter Eleven: Restoring the Lost I**

"How's it going Rodney?" John asked watching as Rodney sighed. "That bad?"

"It's just that all this is horribly complicated," Rodney answered. "I mean I can only work on this on my free time but that free time is dwindling significantly seeing on how we always seem to be off world and—"

"—and I know that you'll get it in the end Rodney." John interrupted. "I have faith in you."

"Oh thanks so much for your vote of confidence."

John smiled and shook his head. "Come one. We have to go."

Rodney looked at John inquisitively. "What for?"

---sparky---

Rodney and John were walking towards the gateroom and Rodney was not pleased. "I don't know what all the fuss is about. If we do this every time someone comes for a visit, we'll never get any work done."

"We're just meeting them at the Gate." John replied.

Rodney shook his head. "We're not just meeting him at the Gate! I've been pulled from my regular duties to help him with his database research! I've got stuff on the go, you know: important, vital projects for the -- the betterment of the human race and your fiancée I might add. I'm never going to figure out how to create human cells that sustain themselves if I have to be a freaking librarian."

John smiled. "Apparently there are other people doing equally important work, Rodney, as hard as that is to believe," and with that they walked into the gateroom and stood on either side of Elizabeth. "Exciting day isn't it?" he asked watching as Elizabeth smiled and nodded once. Rodney for his part grimaced and then before their eyes both Daniel and Vala were beamed down in front of them.

"Daniel, Vala welcome back to Atlantis," Elizabeth stated with a smile.

"Don't you mean Daniel Disneyland?" asked Vala with an arched eyebrow and when she received a quizzical look from her Daniel she just shrugged her shoulders. "What that's what Mitchell calls this place Daniel, you know that."

Daniel smiled warmly at Vala, something that did not escape Elizabeth's notice. "I know," he replied softly before turning back to matters at hand. "Could Vala and I begin at once with Rodney's help?"

Elizabeth nodded. "Of course."

---sparky---

It was hours later and while Vala was doing her best to be as interested in what they were doing she wasn't doing a good enough job with it. Her one consolation was that she was handling herself better than Rodney. "Just get to the point," Rodney snapped.

"Okay," Daniel agreed. "He never talked about it in his entries, but several of Janus' peers suspected he had a "bastion of unfettered thought and experimentation" or -- as one of his lovers put it…"

"Lovers?" asked Rodney. "Janus had lovers?"

"Is it so surprising?" asked Vala with a smirk. "He was a genius."

"…anyways it was an isle of solitude within the city walls," Daniel explained.

Rodney sighed. " Well, that could just mean he's hard to talk to. People say things like that about me all the time."

"Now, none of these writers had any idea where the lab could be, but one of his young assistants recalls a day where Janus turned a corner down a hallway."

"Oh right," Rodney stated with an exasperated sigh. "Today: saw Janus in the hallway." There's a real page turner!"

"He chased after him with a question about his work but when he rounded the corner, Janus was gone. The hallway was a dead end. He had seemingly disappeared and, I think, into his secret lab." Daniel continued ignoring Rodney's attitude.

"Well, did this assistant happen to mention ..."

"... which hallway?" Vala asked as she finished reading over Daniel's shoulder. "Yes, he does. So that means that my Daniel was right and you were wrong."

Rodney scowled at her. "The jury's still out on that one."

---sparky---

"Are you insane?" John asked as he and Elizabeth walked along the corridor. "Going to meet Todd all by yourself?"

"I'm going on the Daedalus John," she pointed out. "I'll be fine."

"But do you really think he's gonna show up, huh, and let you guys try out Doctor Keller's and Caron's gene therapy on a few of his guys?"

Elizabeth shrugged her shoulders. "Who knows? We did hold up our end of the deal."

"Right," John agreed. "He has what he wants. I should go. I know him."

Elizabeth shook her head. "No. This is a diplomatic mission John."

"A militaristic diplomatic mission," he countered.

She smiled softly. "You're my fiancée John and I know that you want to be there but you are still the second in command and the only one who I trust to come after me should something go wrong."

"Do you think that—"

Elizabeth shook her head and kissed John to stop him from worrying. "I don't think that any thing is going to go wrong but it is still better to be prepared."

John sighed. "Just be careful okay?"

Elizabeth nodded. "Okay."

---sparky---

Later, once Daniel and Vala and Rodney had found the lab the three of them were looking around when suddenly out of now where they were all stunned. Vala was the first to awaken and she quickly scrambled over to Daniel. "What happened?" he asked groggily as she handed him his glasses. "We were kidnapped again weren't we."

"Yes," Vala agreed. "We were."

"Ugh.." moaned Rodney as he too came to. "What the hell happened?!"

"We were attacked." Vala pointed out with a smile.

"_That_ much I got, thanks! By who?" Rodney stated and asked irritably.

Vala sighed. "We were kinda hoping you could tell us."

Rodney of course had no idea what was going around and thus the three of them were left to look around the small triangular cell that they were trapped in. "Okay," Rodney began finally. "There is no way this is a coincidence. I mean, we discover Janus' super-secret lab and less than twenty-four hours later a bunch of aliens show up, all guns blazing?! That's odd don't you think?"

Daniel nodded as did Vala. "This is not a coincidence," she stated. "But how are we going to get out of here?"

"And more importantly," Daniel added. "How did they find us?"

Rodney went on to explain his theory of how they were caught and then all three of them were taken by a strange looking being in an exoskeleton like suit. They were told to get the device before them operational and figuring that they had to do something to stall for time they set to it. Vala wasn't much good for anything except helping Rodney and Daniel translate the ancient writing into plain english and sooner than even she expected Rodney had it figured out. "I think I know what this thing does. It's an endgame machine."

"Like in chess?" asked Vala with an intrigued voice.

"How so?" asked Daniel a little more nervously.

"If it works the way I think it does, it would mean the end of the Wraith once and for all." Rodney explained. "This device would stop them dead in their tracks by creating a very specific sub-space static ... uh, turbulence is probably a better way of looking at it…" he paused and noticed the confused faces on both Vala and Daniel. "Okay, look. Um, although they're all based on a fairly similar technological premise, each race has a slightly different type of hyperdrive. Ours are based on the Asgard drive with our own little twist; the Ancients had their own particular system; and the Wraith, again, have their own separate hyperdrive technology. Here at its base level, a hyperdrive allows you to travel great distances by entering and exiting sub-space."

"We know that," Vala assured.

"Okay," Rodney stated. "If this machine is capable of actually functioning safely, it disrupts the very specific sub-space frequencies the Wraith use."

"So they wouldn't be able to engage their hyperdrive." Daniel figured out.

"Well, that's the genius. They _would_ be able to engage their hyperdrives. It's just that their particular channel of sub-space would be destabilised and their ship would be ripped into a million pieces."

Daniel looked at Rodney. "When this device is turned on, every time a Wraith ship enters hyperspace, it self-destructs?" Rodney said nothing but nodded. "It's a pretty effective idea."

"Very effective," Vala agreed. "Too bad we couldn't have used this with the Orii."

"It is very effective," Rodney continued. "I mean, because even if word got back to the other Wraith that the ships should stop using their hyperdrive, they'd be stuck where they were. They'd only be able to travel using sub-light engines."

"And because an Ancient ship's hyperdrives operate on a different frequency of sub-space, the Ancients could fly around the galaxy and pick them off one by one." Daniel interjected.

Yeah, or you just leave 'em to die in the vastness of space," Rodney suggested.

"So, what's the catch?" asked Vala. "There's always a catch."

"Ah, well, the catch is that Janus ran a three day test about ten thousand years ago and then shut the whole project down because of unforeseen side effects which are not clear." Rodney stated. "This thing from Atlantis is the key to the whole shebang. I mean, Janus brought that back with him to Atlantis but kept it connected to the main system here. One won't work without the other. We can probably get it working again, I mean I can get it working again though the question is whether I should."

"Why wouldn't you?" asked Vala. "Don't you want to destroy the wraith?"

The last time I went down this road, I ... I kinda destroyed a solar system." Rodney admitted. "And those unforeseen side effects have me nervous too."

"So what do we do?" asked Vala. "Reason with them?"

Just then as if cued by some cosmic force one of the aliens came in and Daniel began trying to reason with it. "Now, obviously you're excited about the possibility of ending the Wraiths' reign over this galaxy once and for all, but the reality is: this device and this facility were abandoned by their creator for a very good reason. See, uh, it doesn't work -- at least, not safely. (He gestures to Rodney beside him.) That's from what my friend can tell. Look, we share the same goal. Perhaps we have _many_ things in common…" he paused but the alien didn't respond in the slightest. "Look, given the right amount of time, it's possible we could get the device to function safely, but we'd have to contact our people and bring in a much larger science team. See, I'm not _that_ kind of scientist, and my friend here," Daniel continued pointing to Vala. "Isn't that kind of scientist either but Rodney is and uh—"

"Get the device operational within one hour or I will kill her," the alien responded pointing a weapon at Vala who was frozen in place. "Do you understand?" the alien asked again and both Daniel and Vala noticed when Rodney nodded slowly and stated that he did understand. With a satisfied grunt the alien left the three of them alone and Daniel wrapped a protective arm around Vala.

"You're not going to let them kill me are you?" she asked looking frantically between Rodney and Daniel. "Are you?"

Daniel shook his head and held Vala a little closer. "No of course not."

"Of course not," Rodney agreed as he continued on with his work.

"You took long enough to answer,"

"I was just thinking," Daniel assured.

"About what? Losing me?"

Daniel shook his head. "I am not going to lose you. We'll figure something out."

"Then what were you thinking about?"

"I was thinking about the suits," Daniel began. "I mean they're not in battle any more. Originally I thought it was just their version of SWAT gear, but they still have it on. Maybe they're more than just armour; maybe they're some sort of protective suit. Maybe they can't function on our liveable atmosphere."

"Maybe we should just add it to the list of things that have nothing to do with the task at hand," Rodney stated angrily as he continued wading though the information on the consol. "I mean yes the suits might be the key to figuring out who these guys are but I'm trying on working how to get your girlfriend killed."

Daniel looked sharply at Rodney trying not to wake Vala who had fallen asleep out of sheer exhaustion. "She's not my girlfriend,"

Rodney rolled his eyes. "Like I believe that."

"Well you should."

Rodney shook his head. "I spent the better part of three years watching my two best friends dance around their feelings for one another. Believe me. I know how to recognize the signs." Rodney fell silent and continued to work, occasionally glancing out of the corner of his eye at Daniel who was holding a sleeping Vala. Daniel for his part was thinking about Rodney had said. Somewhere deep down inside him he knew that he had to question whether the feelings he held for Vala were purely platonic. After they had defeated the Ori, when she had told him that Tomin had asked her to come back with him Daniel had been deathly afraid of losing her, and then when she had told him that she had no intention of leaving the SGC because for the first time in her life she felt as though she had somewhere to belong, Daniel had felt elated. And not once in the year and a half since had he questioned her decision, or his. As far as Daniel had been concerned he and Vala had been the best of friends. When Sam left to join the Atlantean expedition she told him not to wait too long and he had brushed that comment off and now he couldn't help feel that he had left things too long. 'What if we don't get out of this,' he thought to himself as Rodney continued to work and Vala slept on. 'What if they kill her like they say they are going to do? How will I be able to live with myself knowing full well that I—"

"Done," Rodney stated, snapping Daniel out of his musings. "It wasn't broken like I thought. Janus just shut it down. All we need is _that_, the key from the Atlantis lab and a basic understanding of Janus' coding style and -- here's where I come in again -- the Ancient gene. I mean, we're ... we're ready to roll."

"Vala wake up," Daniel whispered as he turned to Rodney. "You don't have to do this."

"They're going to kill Vala."

"We can find a way out of this."

Vala shook her head hearing the tale end of the conversation. "No. We have to do this. She paused and looked to Daniel. "They are going to come in here and kill me Daniel and then they'll go for you."

"Yeah and then me," Rodney pointed out in a hysterical voice. "And to tell you the truth here, I'm quite fond of me, so we might as well do it, you know, now, while you're still alive, as opposed to ... you know, then."

Daniel sighed. "Alright. Let's do this then."

All three of them held their breath waiting for the room to explode around them once the device had been turned on and it hadn't and they all wondered what was going to happen next.

---

Meanwhile on the bridge of the Daedalus, Elizabeth greeted Todd. "You have an urgent message from your Hive," she explained as she held out an ear piece for him to take. "I assumed you'd want to take it privately." She watched as Todd nodded, took the ear piece, listened carefully and then barked out an order. "What was all that about?" she asked curiously.

"One of our facilities is under attack by a rival Hive. Our two support ships must depart for battle. My Hive will remain here; continue the work with Doctor Keller."

Elizabeth looked at him. "How generous of you Todd to stay here to work with us when your people are in danger…hopefully the two of you will get the job done quickly and then you too can go and join the fight."

Todd nodded and turned to the windshield of the Daedalus to watch his hive go. However as soon as the hive hit the window it exploded. "What the hell happened?" Elizabeth and Steven Caldwell yelled at the same time.

"How did you do that?" Todd asked turning on Elizabeth who just stared at him.

"How did we? Todd we didn't do anything."

Todd glowered at her. "You tricked me."

"I swear that we did no such thing and…"

"And you have found the Attero device." Todd accused angrily.

"Attero device?" Elizabeth asked. "What is that?"

But Todd wasn't having any of it. He stunned everyone on the bridge, including Elizabeth despite the fact that her nanites should have protected her but her close proximity to the device rendered her as helpless as the rest of the crew.

---sparky---

Meanwhile Rodney had just figured out the side effect. "Oh no," he muttered in horror.

"What?" asked Vala as she held her arms across her chest in a defensive pose.

"What is it?" prompted Daniel as he came to stand behind Vala.

"The side effect is something that is going to royally screw the ret of the galaxy," Rodney stated horrified at what he had done. "I have to shut this thing down."

"What does it do Rodney?" asked Daniel with authority.

"It causes Stargates to blow up."

Vala and Daniel felt the colour drain from their faces as they watched Rodney whiten at the thought. "Atlantis," Vala whispered in horror when suddenly the room opened and the three of them found themselves being stunned once again.

---sparky---

Meanwhile, back at Atlantis they were discovering first hand the devastating side effect even though they didn't know what it was. "Everyone who doesn't need to be here, get to the edge of the city. Move! Everybody!" The crew started to scatter and John turned his attention to Teyla. "You're gonna want to get out of here."

"John, I ..."

"Teyla you have a baby to think about," John pointed out angrily. "And you have to tell Elizabeth what happened." For a few breathless seconds John watched the pain of what he was asking her to do cross her face and then unhappily she joined the people fleeing the gateroom and John turned back to Radek. "You can do it, Radek." He encouraged gently. "You can save us all." Radek said nothing but continued to type and the yellow glow of the burning Stargate began to diminish a little. A wave of relief washed over John. "It's going down. We're gonna make it." But then he saw Radek shook his head and utter four words before his world exploded.


	33. Part II: Restoring the Lost II

_Author's Note: No, I'm not dead and yes this story will be officially finished at the end of this chapter. I figured that ending it now was better than leaving it hanging. I am sorry that I didn't finish out the AU version of season five but aside from this two parter and the odd episode I haven't seen anything and so I have no real inspiration to continue it. With this last chapter though, this story is finished and I thank you all for your wonderful reviews. It's really meant a lot to me and I hope that you'll leave one last review, just to let me know what you thought of this final chapter. Take care. ~Anjirika_

**Chapter 12: Restoring the Lost II **

"Move!" Teyla ordered. "Quickly. We have to get everyone to the lower levels of the tower to make sure that everyone will be—" an explosion sounded far above them. People screamed and ducked as the tower shook and the lights flickered. Teyla's first thought was for her friends and she activated her headset radio. "Colonel Sheppard?" she called. "Are you alright?" Teyla waited a couple seconds before calling out again. "John?"

But there was no answer. Teyla flagged down a nurse and together they made their way back up to the control room. They were met with devastation and destruction. Teyla felt as though she would find her teammate dead, but luckily enough both Radek and John were found alive, though John was in serious need for some medical attention.

"You should have been more careful," the nurse was telling John as she was pulling pieces of glass out of his back.

"You should check my job description," John began sarcastically. "Careful is not part of it."

"John," Teyla interjected. "We are setting up an axillary command room."

"Good," John stated with a wince. "And—"

"What happened?"

"I have no idea," John answered. "We'll probably need McKay for this one."

.

Vala huddled up against Daniel while Rodney paced. "Alright," he muttered. "So the device creates a very specific sub-space turbulence that makes it impossible for the Wraith to operate their hyperdrive."

Vala sighed. "You said that already."

"But there's a side effect."

"The unforseen one that Janus mentioned." Daniel stated.

"Yeah well something not seen here because there is no Stargate."

"The point Rodney?" asked Daniel.

And so Rodney explained how the sub space turbulence only affects the Wraiths' hyperdrive systems but it also created a radiation that would mess with the basic operation of all the stargates in the Pegasus network. When Daniel asked what he meant by that, Rodney explained that the gates would overload and explode.

"So what are we supposed to do?" asked Vala.

Rodney shook his head. "I have no idea."

.

Elizabeth was the first one to awaken, something that Todd did not fail to recognize.

"Excellent timing Doctor Weir."

"Whatever it is that you think we've done, I assure you—"

"Take us out of hyperspace," Todd ordered, ignoring Elizabeth completely.

"But we haven't arrived at Atlantis yet."

"Atlantis?" asked Elizabeth, the cold grip of fear settling into her stomach.

"We're within communications range," Todd continued, ignoring Elizabeth once more. "We don't wanna get too close. Take us out." Todd paused and turned to Elizabeth. "I was hoping that you'd be awake for this."

.

John smiled at the screen, unaware of what was going on. "Daedalus it's good to..." he trailed off as he saw Todd sitting on the Daedalus bridge. "What the—?" he asked, feeling as though he had missed something. "What the hell is going on? Where's Caldwell? Where's Elizabeth?"

"Caldwell and the rest of his crew are off duty and as for Doctor Weir," he motioned and Elizabeth was brought to stand before him. "She is right here."

"Elizabeth," John asked, trying to keep his voice level. "You okay?"

"I've been better," she stated honestly.

"Now," Todd began again. "I want you to listen,"

And Todd went onto explain about the Attero device and how the ancients hadn't the stomach to leave it running once they realized what the side effects were. He also gave John the ultimatum that he either gave up the devices location or the entire crew of the Daedalus would be killed, starting with Elizabeth. With that threat, or rather with that promise, the line went dead and John turned to Teyla, fear etched into his eyes.

"What are the odds that the,"

"Attero device?"

"Right," John stated as he turned to Radek. "What are the odds that this thing was at the other end of the sub-space link that Rodney opened when he went to that lab?

"M6H-987? I'd say it's very likely. It's also very likely that's where he Miss Mal Doran and Doctor Jackson were taken." Radek explained.

"It must be a weapon that Janus developed during the Wraith war." Teyla concluded.

"But to blow up stargates?" John asked.

"I doubt that was its original design. It doesn't seem like an effective strategy."

John nodded at Radek's explanation. "So its a nasty side effect. That's probably why they stopped production."

"We must give Todd what he wants," Teyla stated. "He may be able to stop them."

"Yeah," John agreed. "You're right."

.

"Well?" asked Todd as John came back up on the Daedalus's screen.

"We don't have what you need," John answered. "But we can lead you to what you want."

"Oh?" asked Todd, not sounding impressed.

"We were attacked yesterday by aliens that we've never encountered before,"

"A likely story Sheppard,"

"It's the truth," John insisted. "Pick me up and I'll lead you to them."

"You give me the coordinates or I'll kill Doctor Weir before your eyes."

With that threat, John had no choice. He did as Todd commanded.

.

Despite the threat that the Daedalus's crew posed, Todd was able to make it to the planet that John had sent him with no problems. With Elizabeth at his side the wraith beamed into the complex only to be stunned instantly. Elizabeth looked at the strange aliens expecting to be killed but out of nowhere, Daniel, Vala and Rodney appeared.

"Elizabeth?" asked Rodney. "What are you—"

"—you're all alive," she interjected. "Thank god."

"And you'll never believe this Elizabeth," Daniel began with a wide grin on his face. "But these aliens, well we've met their kind before."

"Yes," Vala stated with a smile. "We have."

And so they explained to Elizabeth how the lost tribe of the Asgard race had travelled to the Pegasus galaxy to complete their research in peace and while they weren't willing to be true allies to the humans like their brethren had been— thanks to Daniel's persuading they were willing to help in some matters.

.

Elizabeth returned to Atlantis feeling as though a burden had been lifted off her shoulders and she was so relieved to see that her beloved John had made it through the crisis safe and sound, even if their gateroom hadn't. Before she could have a proper reunion with her fiancee however, she had to see Vala and Daniel off to their home and she couldn't help but notice how they walked through the gate hand in hand.

"Well," John began on their balcony later that night. "That was..."

"Interesting to say the least."

"We got new allies," he continued.

"We did," Elizabeth stated with a smile. "I can't believe it."

"I know," John murmured. "To think that not all of the Asgard are dead and—"

"John," she interjected, lacing her fingers through his. "There's something I've got to tell you."

"Oh?" asked John turning to his fiancee. "What's that?"

Elizabeth kissed John and when she pulled away, she whispered in his ear. "I'm human again."

"Excuse me?" he asked.

"The Asgard," she explained. "They did what Rodney hasn't been able to do. They replaced my metal nanites with organic ones."

"So you're human?"

Elizabeth nodded. "Essentially."

"You're the same old Elizabeth?"

"I'd hardly call myself old John."

He shook his head. "You know what I mean."

"Yes," she laughed. "I do."

.

Little did John and Elizabeth know that their remaining months on Atlantis would be so fraught with peril. There were problems with Michael once again, and John's team was put up for trial but thanks to Elizabeth's negotiating, they were released without incident. And when the enemy came knocking at their gate, they found themselves bringing Atlantis home to protect Earth against the Wraith. On their balcony, overlooking the harbour, John and Elizabeth were married and although the future of Atlantis was unsure, and would probably change daily like the tides, they knew that their relationship would endure.

END


End file.
